| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
| Num | 1 | | ID | task.align_bwa.bwa_aln_rep2.line_111.id_10 | | Name | bwa_aln rep2 | | Thread | thread_42 | | PID | 35894 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-28 23:10:47 | | End | 2017-01-29 03:39:34 | | Elapsed | 04:28:47 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.sai
| | Dependencies | | |
# SYS command. line 113
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 116
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.sai
# SYS command. line 118
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
57260 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 58357482 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz
[main] Real time: 16102.822 sec; CPU: 16085.660 sec
|
| Num | 2 | | ID | task.align_bwa.bwa_aln_rep1.line_111.id_11 | | Name | bwa_aln rep1 | | Thread | thread_41 | | PID | 35895 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-28 23:10:47 | | End | 2017-01-29 04:24:07 | | Elapsed | 05:13:20 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.sai
| | Dependencies | | |
# SYS command. line 113
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 116
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.sai
# SYS command. line 118
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
57259 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.34 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61064961 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz
[main] Real time: 18776.354 sec; CPU: 18757.216 sec
|
| Num | 3 | | ID | task.align_bwa.bwa_aln_ctl1.line_111.id_12 | | Name | bwa_aln ctl1 | | Thread | thread_43 | | PID | 35896 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2017-01-28 23:10:47 | | End | 2017-01-29 06:56:08 | | Elapsed | 07:45:21 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.sai
| | Dependencies | | |
# SYS command. line 113
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 116
bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.sai
# SYS command. line 118
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
57258 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.06 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.04 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.71 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.47 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.56 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.63 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.40 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.04 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.37 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.29 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.14 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.92 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.50 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.60 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.05 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.73 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.75 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.66 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.51 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.89 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.32 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.71 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.73 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.19 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.40 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.43 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.84 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.12 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.51 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.38 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.11 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.03 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.72 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.17 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.98 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.49 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.96 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.28 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.10 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.23 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.12 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.83 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.08 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.89 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.46 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.55 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.95 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.18 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.56 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.43 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.12 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.80 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.49 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.04 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.81 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.35 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.59 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.43 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.02 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.39 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.39 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.67 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.70 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.85 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.43 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.02 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.36 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.57 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.89 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.75 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.53 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.57 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.14 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.36 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.57 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.39 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.27 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.94 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.68 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.42 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.24 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.39 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.63 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.78 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.17 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.18 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.08 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.08 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.17 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.74 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.13 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.40 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.49 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.18 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.41 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.92 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.24 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.80 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.22 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.92 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.74 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.25 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.32 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.99 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.13 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.04 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.97 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.52 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.69 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.30 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.26 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.37 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.33 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.77 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.79 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.31 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.52 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.83 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.04 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.66 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.51 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.52 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.72 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.08 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.40 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.54 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.23 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.39 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.18 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.51 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.19 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.65 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.29 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.31 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.50 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.31 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.79 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.03 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.36 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.20 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.09 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.59 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.52 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.31 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.62 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.59 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.97 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.69 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.77 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.16 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.58 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.53 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.63 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.26 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.92 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.94 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.23 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.79 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.54 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.67 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.49 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.78 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.03 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.89 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.13 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.02 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.52 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.86 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.13 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.22 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.50 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.21 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.12 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.34 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.99 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.24 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.07 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.61 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.07 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.18 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.13 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.47 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.53 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.01 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.26 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.88 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.75 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.67 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.71 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.02 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.74 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.12 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.94 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.78 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.41 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.39 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.62 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.54 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.41 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.70 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.62 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.42 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.36 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.91 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.34 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.13 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.11 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.31 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.70 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.99 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.04 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.81 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.57 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.76 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.86 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.71 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.19 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.18 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.30 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.31 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.64 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.21 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.58 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.28 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.21 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.14 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.85 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.91 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.22 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 105693501 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz
[main] Real time: 27897.276 sec; CPU: 53540.972 sec
|
| Num | 4 | | ID | task.align_bwa.bwa_sam_rep2.line_143.id_13 | | Name | bwa_sam rep2 | | Thread | thread_42 | | PID | 36068 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2017-01-29 03:39:36 | | End | 2017-01-29 05:20:19 | | Elapsed | 01:40:42 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.sai
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.flagstat.qc
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam
# SYS command. line 152
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.flagstat.qc
# SYS command. line 154
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
10349 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.82 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.33 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.02 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.83 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.39 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.43 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.53 sec
[bwa_aln_core] refine gapped alignments... 1.82 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.49 sec
[bwa_aln_core] refine gapped alignments... 2.09 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.68 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.94 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.24 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.60 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.25 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.31 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.59 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.77 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.79 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.19 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.55 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.67 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.65 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.75 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.94 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.78 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.88 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.52 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.68 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.10 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.21 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.95 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.20 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.03 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.99 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.09 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.10 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.94 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.71 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.21 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.95 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.35 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.59 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.78 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.68 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.43 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.00 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.21 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.63 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.97 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.22 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.30 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.58 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.85 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.50 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.37 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.38 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.27 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.22 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.71 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.94 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.09 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.24 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.46 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.39 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.22 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.06 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.89 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.97 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.76 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.68 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.78 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.59 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.48 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.60 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.20 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.92 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.16 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.55 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.48 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.36 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.78 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.72 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.58 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.58 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.17 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.63 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 58357482 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946779.fastq.gz
[main] Real time: 5314.415 sec; CPU: 5062.528 sec
|
| Num | 5 | | ID | task.align_bwa.bwa_sam_rep1.line_143.id_14 | | Name | bwa_sam rep1 | | Thread | thread_41 | | PID | 36069 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2017-01-29 04:24:09 | | End | 2017-01-29 05:01:40 | | Elapsed | 00:37:31 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.sai
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.flagstat.qc
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam
# SYS command. line 152
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.flagstat.qc
# SYS command. line 154
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
5260 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.57 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.91 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.11 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.26 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.38 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.95 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.21 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.57 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.63 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.95 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.08 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.66 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.50 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.51 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.51 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.59 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.77 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.63 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.91 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 61064961 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946778.fastq.gz
[main] Real time: 1504.351 sec; CPU: 1229.624 sec
|
| Num | 6 | | ID | task.postalign_bam.dedup_bam_1_rep1.line_95.id_15 | | Name | dedup_bam_1 rep1 | | Thread | thread_41 | | PID | 36070 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:01:42 | | End | 2017-01-29 05:15:41 | | Elapsed | 00:13:58 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam
| | Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
17370 (process ID) old priority 0, new priority 10
|
| Num | 7 | | ID | task.postalign_bam.markdup_bam_picard_rep1.line_348.id_16 | | Name | markdup_bam_picard rep1 | | Thread | thread_41 | | PID | 36071 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2017-01-29 05:15:43 | | End | 2017-01-29 05:24:52 | | Elapsed | 00:09:09 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.dup.qc
| | Dependencies | | |
# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
10729 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 05:16:06 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 05:16:06 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2017-01-29 05:16:06 MarkDuplicates Start of doWork freeMemory: 254879512; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-29 05:16:06 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-29 05:16:06 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
WARNING 2017-01-29 05:16:07 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1946778.9684944'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2017-01-29 05:16:11 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:52,732,758
INFO 2017-01-29 05:16:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:97,230,944
INFO 2017-01-29 05:16:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:16 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:173,202,542
INFO 2017-01-29 05:16:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:19 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:223,313,198
INFO 2017-01-29 05:16:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:21 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr2:12,109,375
INFO 2017-01-29 05:16:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:23 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr2:71,688,113
INFO 2017-01-29 05:16:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:26 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr2:143,673,199
INFO 2017-01-29 05:16:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:28 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr2:217,475,897
INFO 2017-01-29 05:16:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:30 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr3:26,518,638
INFO 2017-01-29 05:16:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:33 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr3:70,212,652
INFO 2017-01-29 05:16:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:35 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr3:136,677,290
INFO 2017-01-29 05:16:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:37 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr4:13,178,071
INFO 2017-01-29 05:16:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:39 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr4:100,179,890
INFO 2017-01-29 05:16:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:43 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr4:184,476,399
INFO 2017-01-29 05:16:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:46 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr5:66,808,701
INFO 2017-01-29 05:16:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:48 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr5:140,922,889
INFO 2017-01-29 05:16:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:50 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr6:8,286,864
INFO 2017-01-29 05:16:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:52 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr6:78,041,814
INFO 2017-01-29 05:16:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:16:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr6:143,548,276
INFO 2017-01-29 05:16:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:00 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 5s. Last read position: chr7:28,699,690
INFO 2017-01-29 05:17:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 5s. Last read position: chr7:101,780,362
INFO 2017-01-29 05:17:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:08 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr7:156,050,751
INFO 2017-01-29 05:17:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:14 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 6s. Last read position: chr8:71,096,470
INFO 2017-01-29 05:17:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr8:138,942,559
INFO 2017-01-29 05:17:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:24 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 8s. Last read position: chr9:90,709,177
INFO 2017-01-29 05:17:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:28 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: chr10:8,994,427
INFO 2017-01-29 05:17:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:30 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr10:78,871,128
INFO 2017-01-29 05:17:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:34 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 4s. Last read position: chr10:130,217,757
INFO 2017-01-29 05:17:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:36 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr11:65,214,687
INFO 2017-01-29 05:17:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:41 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 5s. Last read position: chr11:126,717,630
INFO 2017-01-29 05:17:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:43 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr12:57,921,490
INFO 2017-01-29 05:17:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:45 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr12:123,563,191
INFO 2017-01-29 05:17:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:56 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 11s. Last read position: chr13:68,083,097
INFO 2017-01-29 05:17:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:17:58 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr14:25,458,494
INFO 2017-01-29 05:17:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:01 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr14:94,546,820
INFO 2017-01-29 05:18:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:03 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr15:82,089,373
INFO 2017-01-29 05:18:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:07 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: chr16:30,874,663
INFO 2017-01-29 05:18:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:09 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr17:9,321,085
INFO 2017-01-29 05:18:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 4s. Last read position: chr17:73,487,783
INFO 2017-01-29 05:18:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr18:52,845,573
INFO 2017-01-29 05:18:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:17 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr19:45,285,688
INFO 2017-01-29 05:18:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 9s. Last read position: chr20:45,468,858
INFO 2017-01-29 05:18:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:29 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr21:45,737,065
INFO 2017-01-29 05:18:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:18:31 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chrX:17,050,408
INFO 2017-01-29 05:18:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:19:02 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 30s. Last read position: chrX:93,969,363
INFO 2017-01-29 05:19:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:19:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chrX:145,782,164
INFO 2017-01-29 05:19:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:19:05 MarkDuplicates Read 46267633 records. 0 pairs never matched.
INFO 2017-01-29 05:19:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 7444883984; totalMemory: 7697072128; maxMemory: 11453595648
INFO 2017-01-29 05:19:06 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-29 05:19:06 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-29 05:19:06 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-29 05:19:17 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-29 05:19:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 5689507720; totalMemory: 8628207616; maxMemory: 11453595648
INFO 2017-01-29 05:19:17 MarkDuplicates Marking 8225621 records as duplicates.
INFO 2017-01-29 05:19:17 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-29 05:20:26 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:09s. Time for last 10,000,000: 69s. Last read position: chr3:70,212,652
INFO 2017-01-29 05:21:38 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:20s. Time for last 10,000,000: 71s. Last read position: chr7:28,699,690
INFO 2017-01-29 05:22:51 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:03:33s. Time for last 10,000,000: 73s. Last read position: chr11:126,717,630
INFO 2017-01-29 05:24:04 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 73s. Last read position: chr18:52,845,573
INFO 2017-01-29 05:24:50 MarkDuplicates Before output close freeMemory: 8594857400; totalMemory: 8675917824; maxMemory: 11453595648
INFO 2017-01-29 05:24:51 MarkDuplicates After output close freeMemory: 8499960216; totalMemory: 8581021696; maxMemory: 11453595648
[Sun Jan 29 05:24:51 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.75 minutes.
Runtime.totalMemory()=8581021696
|
| Num | 8 | | ID | task.postalign_bam.dedup_bam_1_rep2.line_95.id_17 | | Name | dedup_bam_1 rep2 | | Thread | thread_42 | | PID | 36072 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:20:22 | | End | 2017-01-29 05:34:23 | | Elapsed | 00:14:01 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam
| | Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23079 (process ID) old priority 0, new priority 10
|
| Num | 9 | | ID | task.postalign_bam.dedup_bam_2_rep1.line_144.id_18 | | Name | dedup_bam_2 rep1 | | Thread | thread_41 | | PID | 36073 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:24:53 | | End | 2017-01-29 05:36:45 | | Elapsed | 00:11:52 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.pbc.qc
| | Dependencies | | |
# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
37758 (process ID) old priority 0, new priority 10
|
| Num | 10 | | ID | task.postalign_bam.markdup_bam_picard_rep2.line_348.id_19 | | Name | markdup_bam_picard rep2 | | Thread | thread_42 | | PID | 36074 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2017-01-29 05:34:24 | | End | 2017-01-29 05:42:52 | | Elapsed | 00:08:27 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.dup.qc
| | Dependencies | | |
# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
10890 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 05:34:38 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 05:34:38 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2017-01-29 05:34:38 MarkDuplicates Start of doWork freeMemory: 254879512; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-29 05:34:38 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-29 05:34:38 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
WARNING 2017-01-29 05:34:38 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1946779.28075122'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2017-01-29 05:34:43 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:44,497,926
INFO 2017-01-29 05:34:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:34:47 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr1:93,979,452
INFO 2017-01-29 05:34:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:34:51 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: chr1:170,809,177
INFO 2017-01-29 05:34:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:34:54 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: chr1:223,287,788
INFO 2017-01-29 05:34:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:34:57 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr2:10,672,004
INFO 2017-01-29 05:34:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:00 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr2:71,535,377
INFO 2017-01-29 05:35:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:04 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr2:148,202,894
INFO 2017-01-29 05:35:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:06 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr2:224,368,915
INFO 2017-01-29 05:35:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:09 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr3:36,453,024
INFO 2017-01-29 05:35:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:12 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr3:83,195,268
INFO 2017-01-29 05:35:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:16 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr3:155,971,181
INFO 2017-01-29 05:35:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:19 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr4:42,562,398
INFO 2017-01-29 05:35:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:21 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr4:140,734,262
INFO 2017-01-29 05:35:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:24 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr5:33,549,167
INFO 2017-01-29 05:35:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:28 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 4s. Last read position: chr5:122,043,953
INFO 2017-01-29 05:35:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:31 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr5:178,313,973
INFO 2017-01-29 05:35:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:33 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr6:44,976,732
INFO 2017-01-29 05:35:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr6:132,193,962
INFO 2017-01-29 05:35:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:38 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr7:11,051,132
INFO 2017-01-29 05:35:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:41 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr7:84,436,587
INFO 2017-01-29 05:35:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:46 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 4s. Last read position: chr7:150,448,407
INFO 2017-01-29 05:35:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:48 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr8:60,479,264
INFO 2017-01-29 05:35:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:51 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr8:136,264,110
INFO 2017-01-29 05:35:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:53 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr9:91,091,880
INFO 2017-01-29 05:35:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:56 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr10:7,259,773
INFO 2017-01-29 05:35:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:35:58 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr10:75,894,987
INFO 2017-01-29 05:35:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:00 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr10:127,076,814
INFO 2017-01-29 05:36:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:03 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr11:62,988,017
INFO 2017-01-29 05:36:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:05 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr11:126,131,641
INFO 2017-01-29 05:36:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:07 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr12:57,709,944
INFO 2017-01-29 05:36:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:13 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 5s. Last read position: chr12:124,753,654
INFO 2017-01-29 05:36:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:16 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr13:71,571,417
INFO 2017-01-29 05:36:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:18 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr14:38,447,305
INFO 2017-01-29 05:36:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:21 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr14:102,743,498
INFO 2017-01-29 05:36:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:23 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr15:86,992,826
INFO 2017-01-29 05:36:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:26 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr16:48,359,008
INFO 2017-01-29 05:36:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:28 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr17:10,167,780
INFO 2017-01-29 05:36:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:36 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 8s. Last read position: chr17:69,586,539
INFO 2017-01-29 05:36:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:38 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr18:46,553,293
INFO 2017-01-29 05:36:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:40 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr19:36,233,374
INFO 2017-01-29 05:36:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:43 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr20:35,726,363
INFO 2017-01-29 05:36:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:45 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr21:36,870,360
INFO 2017-01-29 05:36:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:48 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr22:45,835,372
INFO 2017-01-29 05:36:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:36:50 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chrX:71,870,779
INFO 2017-01-29 05:36:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:37:21 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 31s. Last read position: chrX:139,336,168
INFO 2017-01-29 05:37:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 05:37:22 MarkDuplicates Read 45310467 records. 0 pairs never matched.
INFO 2017-01-29 05:37:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 6956966376; totalMemory: 7208960000; maxMemory: 11453595648
INFO 2017-01-29 05:37:23 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-29 05:37:23 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-29 05:37:23 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-29 05:37:36 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-29 05:37:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 5703776232; totalMemory: 8642363392; maxMemory: 11453595648
INFO 2017-01-29 05:37:37 MarkDuplicates Marking 11800925 records as duplicates.
INFO 2017-01-29 05:37:37 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-29 05:38:45 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 67s. Last read position: chr3:83,195,268
INFO 2017-01-29 05:39:54 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:16s. Time for last 10,000,000: 68s. Last read position: chr7:84,436,587
INFO 2017-01-29 05:41:03 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:03:25s. Time for last 10,000,000: 69s. Last read position: chr12:57,709,944
INFO 2017-01-29 05:42:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:04:35s. Time for last 10,000,000: 69s. Last read position: chr19:36,233,374
INFO 2017-01-29 05:42:50 MarkDuplicates Before output close freeMemory: 8632265288; totalMemory: 8713142272; maxMemory: 11453595648
INFO 2017-01-29 05:42:51 MarkDuplicates After output close freeMemory: 8536319352; totalMemory: 8617197568; maxMemory: 11453595648
[Sun Jan 29 05:42:51 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.22 minutes.
Runtime.totalMemory()=8617197568
|
| Num | 11 | | ID | task.postalign_bam.bam_to_tag_rep1.line_505.id_20 | | Name | bam_to_tag rep1 | | Thread | thread_41 | | PID | 36075 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:36:47 | | End | 2017-01-29 05:38:35 | | Elapsed | 00:01:48 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
| | Dependencies | | |
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
20706 (process ID) old priority 0, new priority 10
|
| Num | 12 | | ID | task.postalign_bed.subsample_tag_rep1.line_45.id_21 | | Name | subsample_tag rep1 | | Thread | thread_41 | | PID | 36076 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:38:36 | | End | 2017-01-29 05:39:52 | | Elapsed | 00:01:15 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz
| | Dependencies | | |
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26802 (process ID) old priority 0, new priority 10
Waiting for 21 seconds.
|
| Num | 13 | | ID | task.postalign_bed.spr_rep1.line_255.id_22 | | Name | spr rep1 | | Thread | thread_41 | | PID | 36077 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:39:55 | | End | 2017-01-29 05:41:27 | | Elapsed | 00:01:32 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr2/SRR1946778.nodup.pr2.tagAlign.gz
| | Dependencies | | |
# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr2/SRR1946778.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
30985 (process ID) old priority 0, new priority 10
|
| Num | 14 | | ID | task.postalign_bed.xcor_rep1.line_212.id_23 | | Name | xcor rep1 | | Thread | thread_41 | | PID | 36078 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:41:28 | | End | 2017-01-29 06:00:51 | | Elapsed | 00:19:22 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf
| | Dependencies | | |
# SYS command. line 214
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
37089 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.15M.tagAlign.gz
opened /tmp/36078.1.q/RtmptM4L8B/SRR1946778.nodup.15M.tagAlign92e460ff8cc8
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1721764
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.178926314707944,0.178761176169209,0.178613299624671
Top 3 estimates for fragment length 255,270,285
Window half size 590
Phantom peak location 50
Phantom peak Correlation 0.175066
Normalized Strand cross-correlation coefficient (NSC) 1.039203
Relative Strand cross-correlation Coefficient (RSC) 2.335939
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
| Num | 15 | | ID | task.postalign_bam.dedup_bam_2_rep2.line_144.id_24 | | Name | dedup_bam_2 rep2 | | Thread | thread_42 | | PID | 36079 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:42:53 | | End | 2017-01-29 05:53:31 | | Elapsed | 00:10:37 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.pbc.qc
| | Dependencies | | |
# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
41097 (process ID) old priority 0, new priority 10
|
| Num | 16 | | ID | task.postalign_bam.bam_to_tag_rep2.line_505.id_25 | | Name | bam_to_tag rep2 | | Thread | thread_42 | | PID | 36080 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:53:34 | | End | 2017-01-29 05:55:24 | | Elapsed | 00:01:50 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
| | Dependencies | | |
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19966 (process ID) old priority 0, new priority 10
|
| Num | 17 | | ID | task.postalign_bed.subsample_tag_rep2.line_45.id_26 | | Name | subsample_tag rep2 | | Thread | thread_42 | | PID | 36081 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:55:25 | | End | 2017-01-29 05:56:37 | | Elapsed | 00:01:11 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz
| | Dependencies | | |
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
25647 (process ID) old priority 0, new priority 10
Waiting for 24 seconds.
|
| Num | 18 | | ID | task.postalign_bed.spr_rep2.line_255.id_27 | | Name | spr rep2 | | Thread | thread_42 | | PID | 36082 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:56:40 | | End | 2017-01-29 05:58:13 | | Elapsed | 00:01:33 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr2/SRR1946779.nodup.pr2.tagAlign.gz
| | Dependencies | | |
# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr2/SRR1946779.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
29692 (process ID) old priority 0, new priority 10
|
| Num | 19 | | ID | task.postalign_bed.xcor_rep2.line_212.id_28 | | Name | xcor rep2 | | Thread | thread_42 | | PID | 36083 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 05:58:14 | | End | 2017-01-29 06:17:56 | | Elapsed | 00:19:41 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf
| | Dependencies | | |
# SYS command. line 214
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
35390 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.15M.tagAlign.gz
opened /tmp/36083.1.q/Rtmps15VZA/SRR1946779.nodup.15M.tagAlign8c446fcaabd7
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1728912
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.182164001894418,0.182155866590849,0.1819147761162
Top 3 estimates for fragment length 275,290,320
Window half size 660
Phantom peak location 50
Phantom peak Correlation 0.1760504
Normalized Strand cross-correlation coefficient (NSC) 1.053634
Relative Strand cross-correlation Coefficient (RSC) 2.935156
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
| Num | 20 | | ID | task.align_bwa.bwa_sam_ctl1.line_143.id_29 | | Name | bwa_sam ctl1 | | Thread | thread_43 | | PID | 36084 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2017-01-29 06:56:10 | | End | 2017-01-29 12:45:21 | | Elapsed | 05:49:11 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.sai
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.flagstat.qc
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam
# SYS command. line 152
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.flagstat.qc
# SYS command. line 154
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
11221 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.34 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.78 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.70 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.39 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.73 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.30 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.30 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.57 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.02 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.22 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.79 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.49 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.98 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.91 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.17 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.39 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.72 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.60 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.23 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.62 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.01 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.69 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.09 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.40 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.71 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.59 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.00 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.96 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.61 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.68 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.09 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.03 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.79 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.70 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.66 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.02 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.43 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.97 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.35 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.39 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.21 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.58 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.66 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.05 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.61 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.62 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.59 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.57 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.59 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.96 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.77 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.25 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.38 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 68.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.58 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.69 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.43 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.39 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.12 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.74 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.57 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.48 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.32 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.16 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.40 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.38 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.39 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.21 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.20 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.79 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.52 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.82 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.14 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.10 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.39 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.60 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.64 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.63 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.75 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.01 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.27 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.79 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.36 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.70 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.01 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.84 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.60 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 84.25 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.58 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.27 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.93 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.75 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.90 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.67 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.01 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.31 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.41 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.71 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.92 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.26 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.10 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.38 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.95 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.03 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.58 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.14 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.28 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.54 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.60 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.07 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.98 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.20 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.37 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.69 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.78 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.59 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.15 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.44 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.98 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.10 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.59 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.31 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.53 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.58 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.02 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.50 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.49 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.84 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.92 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.48 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.38 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.64 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.06 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.39 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.78 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.75 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.71 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.31 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.34 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.86 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.98 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.01 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.94 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.64 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.75 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.97 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.02 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.10 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.46 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.83 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.92 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.74 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.82 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.60 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.15 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.59 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.97 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.00 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.49 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 80.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.98 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.68 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.36 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.36 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.15 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.33 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.21 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.96 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.41 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.49 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.60 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.89 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.44 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.91 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.51 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.20 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.06 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.56 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.74 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.75 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.71 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.58 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.34 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.21 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.97 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.92 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.31 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.35 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 105693501 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/RawReadsFiles/SRR1946788.fastq.gz
[main] Real time: 20088.314 sec; CPU: 19800.844 sec
|
| Num | 21 | | ID | task.postalign_bam.dedup_bam_1_ctl1.line_95.id_30 | | Name | dedup_bam_1 ctl1 | | Thread | thread_43 | | PID | 36085 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2017-01-29 12:45:24 | | End | 2017-01-29 12:54:20 | | Elapsed | 00:08:56 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam
| | Dependencies | | |
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.bam | \
sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
33530 (process ID) old priority 0, new priority 10
|
| Num | 22 | | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_31 | | Name | markdup_bam_picard ctl1 | | Thread | thread_43 | | PID | 36086 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2017-01-29 12:54:21 | | End | 2017-01-29 13:04:02 | | Elapsed | 00:09:40 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.dup.qc
| | Dependencies | | |
# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12582 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 12:54:38 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 12:54:38 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2017-01-29 12:54:38 MarkDuplicates Start of doWork freeMemory: 254879512; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-29 12:54:38 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-29 12:54:38 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
WARNING 2017-01-29 12:54:38 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1946788.20380108'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2017-01-29 12:54:43 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:28,900,234
INFO 2017-01-29 12:54:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:54:46 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr1:66,969,142
INFO 2017-01-29 12:54:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:54:49 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr1:152,037,575
INFO 2017-01-29 12:54:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:54:53 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: chr1:204,570,217
INFO 2017-01-29 12:54:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:54:56 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:241,208,173
INFO 2017-01-29 12:54:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:54:59 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr2:55,613,238
INFO 2017-01-29 12:54:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:03 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr2:130,744,335
INFO 2017-01-29 12:55:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:05 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr2:217,847,676
INFO 2017-01-29 12:55:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:08 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr3:31,427,331
INFO 2017-01-29 12:55:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:10 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr3:76,924,758
INFO 2017-01-29 12:55:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:12 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr3:134,658,336
INFO 2017-01-29 12:55:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:16 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: chr4:7,644,431
INFO 2017-01-29 12:55:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:19 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr4:108,122,424
INFO 2017-01-29 12:55:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:21 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr5:12,027,600
INFO 2017-01-29 12:55:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:25 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 4s. Last read position: chr5:108,646,604
INFO 2017-01-29 12:55:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:28 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr5:176,398,725
INFO 2017-01-29 12:55:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:30 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr6:38,647,590
INFO 2017-01-29 12:55:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:32 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr6:124,185,917
INFO 2017-01-29 12:55:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:35 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr7:2,757,713
INFO 2017-01-29 12:55:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:39 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 4s. Last read position: chr7:73,561,154
INFO 2017-01-29 12:55:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:41 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr7:139,122,785
INFO 2017-01-29 12:55:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:48 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 7s. Last read position: chr8:42,044,232
INFO 2017-01-29 12:55:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:52 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr8:126,378,023
INFO 2017-01-29 12:55:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:54 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr9:84,162,695
INFO 2017-01-29 12:55:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:55:59 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 4s. Last read position: chr9:133,702,504
INFO 2017-01-29 12:55:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:01 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr10:45,065,818
INFO 2017-01-29 12:56:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:06 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 4s. Last read position: chr10:102,813,092
INFO 2017-01-29 12:56:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:08 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr11:24,879,392
INFO 2017-01-29 12:56:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:15 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 6s. Last read position: chr11:77,481,707
INFO 2017-01-29 12:56:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:17 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr12:15,984,239
INFO 2017-01-29 12:56:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:26 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 9s. Last read position: chr12:89,608,554
INFO 2017-01-29 12:56:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:28 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr13:21,495,408
INFO 2017-01-29 12:56:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:35 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 6s. Last read position: chr13:84,158,033
INFO 2017-01-29 12:56:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:37 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr14:61,660,857
INFO 2017-01-29 12:56:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:42 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 5s. Last read position: chr15:41,520,275
INFO 2017-01-29 12:56:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:44 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr15:90,889,888
INFO 2017-01-29 12:56:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:46 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr16:30,698,699
INFO 2017-01-29 12:56:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:52 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 5s. Last read position: chr16:87,591,093
INFO 2017-01-29 12:56:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:56:54 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr17:35,641,395
INFO 2017-01-29 12:56:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:03 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 9s. Last read position: chr17:74,127,181
INFO 2017-01-29 12:57:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:05 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr18:35,283,314
INFO 2017-01-29 12:57:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:07 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr19:10,607,597
INFO 2017-01-29 12:57:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:10 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr19:44,016,520
INFO 2017-01-29 12:57:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:12 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr20:33,502,675
INFO 2017-01-29 12:57:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:45 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 33s. Last read position: chr21:31,229,604
INFO 2017-01-29 12:57:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:47 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr22:30,479,810
INFO 2017-01-29 12:57:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:49 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chrX:18,797,961
INFO 2017-01-29 12:57:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:52 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chrX:98,549,375
INFO 2017-01-29 12:57:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:54 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chrM:11
INFO 2017-01-29 12:57:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 12:57:58 MarkDuplicates Read 49731572 records. 0 pairs never matched.
INFO 2017-01-29 12:57:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 7172262040; totalMemory: 7427063808; maxMemory: 11453595648
INFO 2017-01-29 12:57:59 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-29 12:58:00 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-29 12:58:00 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-29 12:58:12 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-29 12:58:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 5714721152; totalMemory: 8655470592; maxMemory: 11453595648
INFO 2017-01-29 12:58:12 MarkDuplicates Marking 6076325 records as duplicates.
INFO 2017-01-29 12:58:12 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-29 12:59:21 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:08s. Time for last 10,000,000: 68s. Last read position: chr3:76,924,758
INFO 2017-01-29 13:00:31 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 70s. Last read position: chr7:73,561,154
INFO 2017-01-29 13:01:41 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:03:28s. Time for last 10,000,000: 70s. Last read position: chr12:15,984,239
INFO 2017-01-29 13:02:52 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:04:39s. Time for last 10,000,000: 70s. Last read position: chr17:74,127,181
INFO 2017-01-29 13:04:00 MarkDuplicates Before output close freeMemory: 8641209728; totalMemory: 8724152320; maxMemory: 11453595648
INFO 2017-01-29 13:04:01 MarkDuplicates After output close freeMemory: 8567808352; totalMemory: 8650752000; maxMemory: 11453595648
[Sun Jan 29 13:04:01 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 9.39 minutes.
Runtime.totalMemory()=8650752000
|
| Num | 23 | | ID | task.postalign_bam.dedup_bam_2_ctl1.line_144.id_32 | | Name | dedup_bam_2 ctl1 | | Thread | thread_43 | | PID | 36087 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2017-01-29 13:04:03 | | End | 2017-01-29 13:15:03 | | Elapsed | 00:11:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.nodup.pbc.qc
| | Dependencies | | |
# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam
# SYS command. line 153
sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam
# SYS command. line 155
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/ctl1/SRR1946788.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
39099 (process ID) old priority 0, new priority 10
|
| Num | 24 | | ID | task.postalign_bam.bam_to_tag_ctl1.line_505.id_33 | | Name | bam_to_tag ctl1 | | Thread | thread_43 | | PID | 36088 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:15:05 | | End | 2017-01-29 13:17:12 | | Elapsed | 00:02:07 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Dependencies | | |
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12755 (process ID) old priority 0, new priority 10
|
| Num | 25 | | ID | task.postalign_bed.pool_tag_pooled_rep.line_436.id_34 | | Name | pool_tag pooled_rep | | Thread | thread_Root | | PID | 36089 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:17:14 | | End | 2017-01-29 13:18:58 | | Elapsed | 00:01:44 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz
| | Dependencies | | |
# SYS command. line 438
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 440
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz
# SYS command. line 442
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12869 (process ID) old priority 0, new priority 10
|
| Num | 26 | | ID | task.postalign_bed.pool_tag_ppr1.line_436.id_35 | | Name | pool_tag ppr1 | | Thread | thread_Root | | PID | 36090 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:17:15 | | End | 2017-01-29 13:18:36 | | Elapsed | 00:01:21 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.pr1.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz
| | Dependencies | | |
# SYS command. line 438
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 440
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr1/SRR1946778.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr1/SRR1946779.nodup.pr1.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz
# SYS command. line 442
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12867 (process ID) old priority 0, new priority 10
Waiting for 10 seconds.
|
| Num | 27 | | ID | task.postalign_bed.pool_tag_ppr2.line_436.id_36 | | Name | pool_tag ppr2 | | Thread | thread_Root | | PID | 36091 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:17:16 | | End | 2017-01-29 13:18:38 | | Elapsed | 00:01:22 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr2/SRR1946778.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr2/SRR1946779.nodup.pr2.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz
| | Dependencies | | |
# SYS command. line 438
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 440
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep1/pr2/SRR1946778.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pseudo_reps/rep2/pr2/SRR1946779.nodup.pr2.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz
# SYS command. line 442
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
12868 (process ID) old priority 0, new priority 10
Waiting for 11 seconds.
|
| Num | 28 | | ID | task.callpeak_macs2.macs2_pooled_rep.line_71.id_37 | | Name | macs2 pooled_rep | | Thread | thread_Root | | PID | 36092 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:19:00 | | End | 2017-01-29 14:48:56 | | Elapsed | 01:29:55 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep -o "SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep -o "SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
13083 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 13:19:25:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 13:19:25: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:19:25: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:19:26: 1000000
INFO @ Sun, 29 Jan 2017 13:19:28: 2000000
INFO @ Sun, 29 Jan 2017 13:19:29: 3000000
INFO @ Sun, 29 Jan 2017 13:19:31: 4000000
INFO @ Sun, 29 Jan 2017 13:19:32: 5000000
INFO @ Sun, 29 Jan 2017 13:19:34: 6000000
INFO @ Sun, 29 Jan 2017 13:19:35: 7000000
INFO @ Sun, 29 Jan 2017 13:19:37: 8000000
INFO @ Sun, 29 Jan 2017 13:19:38: 9000000
INFO @ Sun, 29 Jan 2017 13:19:39: 10000000
INFO @ Sun, 29 Jan 2017 13:19:41: 11000000
INFO @ Sun, 29 Jan 2017 13:19:42: 12000000
INFO @ Sun, 29 Jan 2017 13:19:44: 13000000
INFO @ Sun, 29 Jan 2017 13:19:45: 14000000
INFO @ Sun, 29 Jan 2017 13:19:47: 15000000
INFO @ Sun, 29 Jan 2017 13:19:48: 16000000
INFO @ Sun, 29 Jan 2017 13:19:50: 17000000
INFO @ Sun, 29 Jan 2017 13:19:51: 18000000
INFO @ Sun, 29 Jan 2017 13:19:53: 19000000
INFO @ Sun, 29 Jan 2017 13:19:54: 20000000
INFO @ Sun, 29 Jan 2017 13:19:56: 21000000
INFO @ Sun, 29 Jan 2017 13:19:57: 22000000
INFO @ Sun, 29 Jan 2017 13:19:58: 23000000
INFO @ Sun, 29 Jan 2017 13:20:00: 24000000
INFO @ Sun, 29 Jan 2017 13:20:01: 25000000
INFO @ Sun, 29 Jan 2017 13:20:03: 26000000
INFO @ Sun, 29 Jan 2017 13:20:04: 27000000
INFO @ Sun, 29 Jan 2017 13:20:06: 28000000
INFO @ Sun, 29 Jan 2017 13:20:08: 29000000
INFO @ Sun, 29 Jan 2017 13:20:10: 30000000
INFO @ Sun, 29 Jan 2017 13:20:11: 31000000
INFO @ Sun, 29 Jan 2017 13:20:13: 32000000
INFO @ Sun, 29 Jan 2017 13:20:15: 33000000
INFO @ Sun, 29 Jan 2017 13:20:16: 34000000
INFO @ Sun, 29 Jan 2017 13:20:18: 35000000
INFO @ Sun, 29 Jan 2017 13:20:19: 36000000
INFO @ Sun, 29 Jan 2017 13:20:21: 37000000
INFO @ Sun, 29 Jan 2017 13:20:22: 38000000
INFO @ Sun, 29 Jan 2017 13:20:24: 39000000
INFO @ Sun, 29 Jan 2017 13:20:25: 40000000
INFO @ Sun, 29 Jan 2017 13:20:27: 41000000
INFO @ Sun, 29 Jan 2017 13:20:28: 42000000
INFO @ Sun, 29 Jan 2017 13:20:30: 43000000
INFO @ Sun, 29 Jan 2017 13:20:32: 44000000
INFO @ Sun, 29 Jan 2017 13:20:33: 45000000
INFO @ Sun, 29 Jan 2017 13:20:35: 46000000
INFO @ Sun, 29 Jan 2017 13:20:36: 47000000
INFO @ Sun, 29 Jan 2017 13:20:38: 48000000
INFO @ Sun, 29 Jan 2017 13:20:39: 49000000
INFO @ Sun, 29 Jan 2017 13:20:40: 50000000
INFO @ Sun, 29 Jan 2017 13:20:42: 51000000
INFO @ Sun, 29 Jan 2017 13:20:43: 52000000
INFO @ Sun, 29 Jan 2017 13:20:45: 53000000
INFO @ Sun, 29 Jan 2017 13:20:46: 54000000
INFO @ Sun, 29 Jan 2017 13:20:48: 55000000
INFO @ Sun, 29 Jan 2017 13:20:49: 56000000
INFO @ Sun, 29 Jan 2017 13:20:51: 57000000
INFO @ Sun, 29 Jan 2017 13:20:53: 58000000
INFO @ Sun, 29 Jan 2017 13:20:54: 59000000
INFO @ Sun, 29 Jan 2017 13:20:56: 60000000
INFO @ Sun, 29 Jan 2017 13:20:57: 61000000
INFO @ Sun, 29 Jan 2017 13:20:59: 62000000
INFO @ Sun, 29 Jan 2017 13:21:00: 63000000
INFO @ Sun, 29 Jan 2017 13:21:02: 64000000
INFO @ Sun, 29 Jan 2017 13:21:03: 65000000
INFO @ Sun, 29 Jan 2017 13:21:05: 66000000
INFO @ Sun, 29 Jan 2017 13:21:06: 67000000
INFO @ Sun, 29 Jan 2017 13:21:08: 68000000
INFO @ Sun, 29 Jan 2017 13:21:09: 69000000
INFO @ Sun, 29 Jan 2017 13:21:11: 70000000
INFO @ Sun, 29 Jan 2017 13:21:12: 71000000
INFO @ Sun, 29 Jan 2017 13:21:15: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:21:17: 1000000
INFO @ Sun, 29 Jan 2017 13:21:19: 2000000
INFO @ Sun, 29 Jan 2017 13:21:20: 3000000
INFO @ Sun, 29 Jan 2017 13:21:21: 4000000
INFO @ Sun, 29 Jan 2017 13:21:23: 5000000
INFO @ Sun, 29 Jan 2017 13:21:24: 6000000
INFO @ Sun, 29 Jan 2017 13:21:26: 7000000
INFO @ Sun, 29 Jan 2017 13:21:27: 8000000
INFO @ Sun, 29 Jan 2017 13:21:29: 9000000
INFO @ Sun, 29 Jan 2017 13:21:30: 10000000
INFO @ Sun, 29 Jan 2017 13:21:31: 11000000
INFO @ Sun, 29 Jan 2017 13:21:33: 12000000
INFO @ Sun, 29 Jan 2017 13:21:35: 13000000
INFO @ Sun, 29 Jan 2017 13:21:37: 14000000
INFO @ Sun, 29 Jan 2017 13:21:38: 15000000
INFO @ Sun, 29 Jan 2017 13:21:40: 16000000
INFO @ Sun, 29 Jan 2017 13:21:42: 17000000
INFO @ Sun, 29 Jan 2017 13:21:43: 18000000
INFO @ Sun, 29 Jan 2017 13:21:45: 19000000
INFO @ Sun, 29 Jan 2017 13:21:46: 20000000
INFO @ Sun, 29 Jan 2017 13:21:47: 21000000
INFO @ Sun, 29 Jan 2017 13:21:49: 22000000
INFO @ Sun, 29 Jan 2017 13:21:51: 23000000
INFO @ Sun, 29 Jan 2017 13:21:52: 24000000
INFO @ Sun, 29 Jan 2017 13:21:54: 25000000
INFO @ Sun, 29 Jan 2017 13:21:55: 26000000
INFO @ Sun, 29 Jan 2017 13:21:56: 27000000
INFO @ Sun, 29 Jan 2017 13:21:58: 28000000
INFO @ Sun, 29 Jan 2017 13:21:59: 29000000
INFO @ Sun, 29 Jan 2017 13:22:01: 30000000
INFO @ Sun, 29 Jan 2017 13:22:03: 31000000
INFO @ Sun, 29 Jan 2017 13:22:04: 32000000
INFO @ Sun, 29 Jan 2017 13:22:05: 33000000
INFO @ Sun, 29 Jan 2017 13:22:07: 34000000
INFO @ Sun, 29 Jan 2017 13:22:08: 35000000
INFO @ Sun, 29 Jan 2017 13:22:10: 36000000
INFO @ Sun, 29 Jan 2017 13:22:11: 37000000
INFO @ Sun, 29 Jan 2017 13:22:13: 38000000
INFO @ Sun, 29 Jan 2017 13:22:14: 39000000
INFO @ Sun, 29 Jan 2017 13:22:16: 40000000
INFO @ Sun, 29 Jan 2017 13:22:17: 41000000
INFO @ Sun, 29 Jan 2017 13:22:19: 42000000
INFO @ Sun, 29 Jan 2017 13:22:20: 43000000
INFO @ Sun, 29 Jan 2017 13:22:22: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:22:22: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:22:22: #1 total tags in treatment: 71551554
INFO @ Sun, 29 Jan 2017 13:22:22: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:22:22: #1 finished!
INFO @ Sun, 29 Jan 2017 13:22:22: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:22:22: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:22:22: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:22:22: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:22:22: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 13:22:22: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:27:22: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 13:27:22: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 13:27:22: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 13:27:22: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 13:27:22: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:36:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:36:17: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 13:36:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 13:36:19: Done!
INFO @ Sun, 29 Jan 2017 13:36:24:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 13:36:24: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:36:24: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:36:25: 1000000
INFO @ Sun, 29 Jan 2017 13:36:27: 2000000
INFO @ Sun, 29 Jan 2017 13:36:28: 3000000
INFO @ Sun, 29 Jan 2017 13:36:30: 4000000
INFO @ Sun, 29 Jan 2017 13:36:31: 5000000
INFO @ Sun, 29 Jan 2017 13:36:32: 6000000
INFO @ Sun, 29 Jan 2017 13:36:34: 7000000
INFO @ Sun, 29 Jan 2017 13:36:35: 8000000
INFO @ Sun, 29 Jan 2017 13:36:36: 9000000
INFO @ Sun, 29 Jan 2017 13:36:38: 10000000
INFO @ Sun, 29 Jan 2017 13:36:39: 11000000
INFO @ Sun, 29 Jan 2017 13:36:40: 12000000
INFO @ Sun, 29 Jan 2017 13:36:42: 13000000
INFO @ Sun, 29 Jan 2017 13:36:43: 14000000
INFO @ Sun, 29 Jan 2017 13:36:44: 15000000
INFO @ Sun, 29 Jan 2017 13:36:46: 16000000
INFO @ Sun, 29 Jan 2017 13:36:47: 17000000
INFO @ Sun, 29 Jan 2017 13:36:48: 18000000
INFO @ Sun, 29 Jan 2017 13:36:50: 19000000
INFO @ Sun, 29 Jan 2017 13:36:51: 20000000
INFO @ Sun, 29 Jan 2017 13:36:53: 21000000
INFO @ Sun, 29 Jan 2017 13:36:54: 22000000
INFO @ Sun, 29 Jan 2017 13:36:55: 23000000
INFO @ Sun, 29 Jan 2017 13:36:57: 24000000
INFO @ Sun, 29 Jan 2017 13:36:58: 25000000
INFO @ Sun, 29 Jan 2017 13:36:59: 26000000
INFO @ Sun, 29 Jan 2017 13:37:01: 27000000
INFO @ Sun, 29 Jan 2017 13:37:02: 28000000
INFO @ Sun, 29 Jan 2017 13:37:03: 29000000
INFO @ Sun, 29 Jan 2017 13:37:05: 30000000
INFO @ Sun, 29 Jan 2017 13:37:06: 31000000
INFO @ Sun, 29 Jan 2017 13:37:07: 32000000
INFO @ Sun, 29 Jan 2017 13:37:08: 33000000
INFO @ Sun, 29 Jan 2017 13:37:10: 34000000
INFO @ Sun, 29 Jan 2017 13:37:11: 35000000
INFO @ Sun, 29 Jan 2017 13:37:12: 36000000
INFO @ Sun, 29 Jan 2017 13:37:14: 37000000
INFO @ Sun, 29 Jan 2017 13:37:15: 38000000
INFO @ Sun, 29 Jan 2017 13:37:16: 39000000
INFO @ Sun, 29 Jan 2017 13:37:18: 40000000
INFO @ Sun, 29 Jan 2017 13:37:19: 41000000
INFO @ Sun, 29 Jan 2017 13:37:20: 42000000
INFO @ Sun, 29 Jan 2017 13:37:22: 43000000
INFO @ Sun, 29 Jan 2017 13:37:23: 44000000
INFO @ Sun, 29 Jan 2017 13:37:24: 45000000
INFO @ Sun, 29 Jan 2017 13:37:26: 46000000
INFO @ Sun, 29 Jan 2017 13:37:27: 47000000
INFO @ Sun, 29 Jan 2017 13:37:28: 48000000
INFO @ Sun, 29 Jan 2017 13:37:30: 49000000
INFO @ Sun, 29 Jan 2017 13:37:31: 50000000
INFO @ Sun, 29 Jan 2017 13:37:32: 51000000
INFO @ Sun, 29 Jan 2017 13:37:33: 52000000
INFO @ Sun, 29 Jan 2017 13:37:35: 53000000
INFO @ Sun, 29 Jan 2017 13:37:36: 54000000
INFO @ Sun, 29 Jan 2017 13:37:37: 55000000
INFO @ Sun, 29 Jan 2017 13:37:39: 56000000
INFO @ Sun, 29 Jan 2017 13:37:40: 57000000
INFO @ Sun, 29 Jan 2017 13:37:41: 58000000
INFO @ Sun, 29 Jan 2017 13:37:43: 59000000
INFO @ Sun, 29 Jan 2017 13:37:44: 60000000
INFO @ Sun, 29 Jan 2017 13:37:45: 61000000
INFO @ Sun, 29 Jan 2017 13:37:47: 62000000
INFO @ Sun, 29 Jan 2017 13:37:48: 63000000
INFO @ Sun, 29 Jan 2017 13:37:49: 64000000
INFO @ Sun, 29 Jan 2017 13:37:51: 65000000
INFO @ Sun, 29 Jan 2017 13:37:52: 66000000
INFO @ Sun, 29 Jan 2017 13:37:53: 67000000
INFO @ Sun, 29 Jan 2017 13:37:54: 68000000
INFO @ Sun, 29 Jan 2017 13:37:56: 69000000
INFO @ Sun, 29 Jan 2017 13:37:57: 70000000
INFO @ Sun, 29 Jan 2017 13:37:58: 71000000
INFO @ Sun, 29 Jan 2017 13:38:01: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:38:02: 1000000
INFO @ Sun, 29 Jan 2017 13:38:04: 2000000
INFO @ Sun, 29 Jan 2017 13:38:05: 3000000
INFO @ Sun, 29 Jan 2017 13:38:06: 4000000
INFO @ Sun, 29 Jan 2017 13:38:08: 5000000
INFO @ Sun, 29 Jan 2017 13:38:09: 6000000
INFO @ Sun, 29 Jan 2017 13:38:10: 7000000
INFO @ Sun, 29 Jan 2017 13:38:12: 8000000
INFO @ Sun, 29 Jan 2017 13:38:13: 9000000
INFO @ Sun, 29 Jan 2017 13:38:14: 10000000
INFO @ Sun, 29 Jan 2017 13:38:15: 11000000
INFO @ Sun, 29 Jan 2017 13:38:17: 12000000
INFO @ Sun, 29 Jan 2017 13:38:18: 13000000
INFO @ Sun, 29 Jan 2017 13:38:19: 14000000
INFO @ Sun, 29 Jan 2017 13:38:21: 15000000
INFO @ Sun, 29 Jan 2017 13:38:22: 16000000
INFO @ Sun, 29 Jan 2017 13:38:23: 17000000
INFO @ Sun, 29 Jan 2017 13:38:24: 18000000
INFO @ Sun, 29 Jan 2017 13:38:26: 19000000
INFO @ Sun, 29 Jan 2017 13:38:27: 20000000
INFO @ Sun, 29 Jan 2017 13:38:28: 21000000
INFO @ Sun, 29 Jan 2017 13:38:30: 22000000
INFO @ Sun, 29 Jan 2017 13:38:31: 23000000
INFO @ Sun, 29 Jan 2017 13:38:32: 24000000
INFO @ Sun, 29 Jan 2017 13:38:34: 25000000
INFO @ Sun, 29 Jan 2017 13:38:35: 26000000
INFO @ Sun, 29 Jan 2017 13:38:36: 27000000
INFO @ Sun, 29 Jan 2017 13:38:37: 28000000
INFO @ Sun, 29 Jan 2017 13:38:39: 29000000
INFO @ Sun, 29 Jan 2017 13:38:40: 30000000
INFO @ Sun, 29 Jan 2017 13:38:41: 31000000
INFO @ Sun, 29 Jan 2017 13:38:42: 32000000
INFO @ Sun, 29 Jan 2017 13:38:44: 33000000
INFO @ Sun, 29 Jan 2017 13:38:45: 34000000
INFO @ Sun, 29 Jan 2017 13:38:46: 35000000
INFO @ Sun, 29 Jan 2017 13:38:48: 36000000
INFO @ Sun, 29 Jan 2017 13:38:49: 37000000
INFO @ Sun, 29 Jan 2017 13:38:50: 38000000
INFO @ Sun, 29 Jan 2017 13:38:51: 39000000
INFO @ Sun, 29 Jan 2017 13:38:53: 40000000
INFO @ Sun, 29 Jan 2017 13:38:54: 41000000
INFO @ Sun, 29 Jan 2017 13:38:55: 42000000
INFO @ Sun, 29 Jan 2017 13:38:57: 43000000
INFO @ Sun, 29 Jan 2017 13:38:58: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:38:58: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:38:58: #1 total tags in treatment: 71551554
INFO @ Sun, 29 Jan 2017 13:38:58: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:38:58: #1 finished!
INFO @ Sun, 29 Jan 2017 13:38:58: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:38:58: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:38:58: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:38:58: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:38:58: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 13:38:58: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:43:03: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:46:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:46:22: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 13:46:23: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 13:46:25: Done!
INFO @ Sun, 29 Jan 2017 13:46:30: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 13:48:38: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 13:50:09: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 13:51:35: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 29 Jan 2017 13:59:43: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 14:05:45: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_FE.bdg'!
INFO @ Sun, 29 Jan 2017 14:20:20: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 14:22:28: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 14:24:00: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 14:24:59: Values in your input bedGraph files will be multiplied by 43.655247 ...
INFO @ Sun, 29 Jan 2017 14:34:03: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Sun, 29 Jan 2017 14:35:03: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 14:38:39: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_ppois.bdg'!
|
| Num | 29 | | ID | task.callpeak_macs2.macs2_ppr1.line_71.id_38 | | Name | macs2 ppr1 | | Thread | thread_Root | | PID | 36093 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:19:01 | | End | 2017-01-29 13:42:07 | | Elapsed | 00:23:06 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
13082 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 13:19:24:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 13:19:24: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:19:24: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:19:27: 1000000
INFO @ Sun, 29 Jan 2017 13:19:28: 2000000
INFO @ Sun, 29 Jan 2017 13:19:30: 3000000
INFO @ Sun, 29 Jan 2017 13:19:32: 4000000
INFO @ Sun, 29 Jan 2017 13:19:33: 5000000
INFO @ Sun, 29 Jan 2017 13:19:35: 6000000
INFO @ Sun, 29 Jan 2017 13:19:37: 7000000
INFO @ Sun, 29 Jan 2017 13:19:38: 8000000
INFO @ Sun, 29 Jan 2017 13:19:40: 9000000
INFO @ Sun, 29 Jan 2017 13:19:41: 10000000
INFO @ Sun, 29 Jan 2017 13:19:43: 11000000
INFO @ Sun, 29 Jan 2017 13:19:44: 12000000
INFO @ Sun, 29 Jan 2017 13:19:46: 13000000
INFO @ Sun, 29 Jan 2017 13:19:48: 14000000
INFO @ Sun, 29 Jan 2017 13:19:49: 15000000
INFO @ Sun, 29 Jan 2017 13:19:51: 16000000
INFO @ Sun, 29 Jan 2017 13:19:53: 17000000
INFO @ Sun, 29 Jan 2017 13:19:54: 18000000
INFO @ Sun, 29 Jan 2017 13:19:56: 19000000
INFO @ Sun, 29 Jan 2017 13:19:58: 20000000
INFO @ Sun, 29 Jan 2017 13:19:59: 21000000
INFO @ Sun, 29 Jan 2017 13:20:01: 22000000
INFO @ Sun, 29 Jan 2017 13:20:02: 23000000
INFO @ Sun, 29 Jan 2017 13:20:04: 24000000
INFO @ Sun, 29 Jan 2017 13:20:05: 25000000
INFO @ Sun, 29 Jan 2017 13:20:07: 26000000
INFO @ Sun, 29 Jan 2017 13:20:08: 27000000
INFO @ Sun, 29 Jan 2017 13:20:10: 28000000
INFO @ Sun, 29 Jan 2017 13:20:11: 29000000
INFO @ Sun, 29 Jan 2017 13:20:13: 30000000
INFO @ Sun, 29 Jan 2017 13:20:14: 31000000
INFO @ Sun, 29 Jan 2017 13:20:16: 32000000
INFO @ Sun, 29 Jan 2017 13:20:17: 33000000
INFO @ Sun, 29 Jan 2017 13:20:19: 34000000
INFO @ Sun, 29 Jan 2017 13:20:20: 35000000
INFO @ Sun, 29 Jan 2017 13:20:24: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:20:26: 1000000
INFO @ Sun, 29 Jan 2017 13:20:27: 2000000
INFO @ Sun, 29 Jan 2017 13:20:29: 3000000
INFO @ Sun, 29 Jan 2017 13:20:30: 4000000
INFO @ Sun, 29 Jan 2017 13:20:32: 5000000
INFO @ Sun, 29 Jan 2017 13:20:33: 6000000
INFO @ Sun, 29 Jan 2017 13:20:35: 7000000
INFO @ Sun, 29 Jan 2017 13:20:36: 8000000
INFO @ Sun, 29 Jan 2017 13:20:37: 9000000
INFO @ Sun, 29 Jan 2017 13:20:39: 10000000
INFO @ Sun, 29 Jan 2017 13:20:40: 11000000
INFO @ Sun, 29 Jan 2017 13:20:42: 12000000
INFO @ Sun, 29 Jan 2017 13:20:43: 13000000
INFO @ Sun, 29 Jan 2017 13:20:45: 14000000
INFO @ Sun, 29 Jan 2017 13:20:46: 15000000
INFO @ Sun, 29 Jan 2017 13:20:48: 16000000
INFO @ Sun, 29 Jan 2017 13:20:49: 17000000
INFO @ Sun, 29 Jan 2017 13:20:51: 18000000
INFO @ Sun, 29 Jan 2017 13:20:52: 19000000
INFO @ Sun, 29 Jan 2017 13:20:54: 20000000
INFO @ Sun, 29 Jan 2017 13:20:55: 21000000
INFO @ Sun, 29 Jan 2017 13:20:57: 22000000
INFO @ Sun, 29 Jan 2017 13:20:58: 23000000
INFO @ Sun, 29 Jan 2017 13:20:59: 24000000
INFO @ Sun, 29 Jan 2017 13:21:01: 25000000
INFO @ Sun, 29 Jan 2017 13:21:02: 26000000
INFO @ Sun, 29 Jan 2017 13:21:04: 27000000
INFO @ Sun, 29 Jan 2017 13:21:05: 28000000
INFO @ Sun, 29 Jan 2017 13:21:07: 29000000
INFO @ Sun, 29 Jan 2017 13:21:08: 30000000
INFO @ Sun, 29 Jan 2017 13:21:10: 31000000
INFO @ Sun, 29 Jan 2017 13:21:11: 32000000
INFO @ Sun, 29 Jan 2017 13:21:13: 33000000
INFO @ Sun, 29 Jan 2017 13:21:14: 34000000
INFO @ Sun, 29 Jan 2017 13:21:16: 35000000
INFO @ Sun, 29 Jan 2017 13:21:17: 36000000
INFO @ Sun, 29 Jan 2017 13:21:19: 37000000
INFO @ Sun, 29 Jan 2017 13:21:20: 38000000
INFO @ Sun, 29 Jan 2017 13:21:22: 39000000
INFO @ Sun, 29 Jan 2017 13:21:23: 40000000
INFO @ Sun, 29 Jan 2017 13:21:25: 41000000
INFO @ Sun, 29 Jan 2017 13:21:26: 42000000
INFO @ Sun, 29 Jan 2017 13:21:28: 43000000
INFO @ Sun, 29 Jan 2017 13:21:29: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:21:29: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:21:29: #1 total tags in treatment: 35775777
INFO @ Sun, 29 Jan 2017 13:21:29: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:21:29: #1 finished!
INFO @ Sun, 29 Jan 2017 13:21:29: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:21:29: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:21:29: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:21:29: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:21:29: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 13:21:29: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:25:45: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 13:25:45: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 13:25:45: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 13:25:45: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 13:25:45: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:32:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:32:45: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 13:32:46: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 13:32:47: Done!
INFO @ Sun, 29 Jan 2017 13:32:51:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 13:32:51: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:32:51: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:32:53: 1000000
INFO @ Sun, 29 Jan 2017 13:32:54: 2000000
INFO @ Sun, 29 Jan 2017 13:32:56: 3000000
INFO @ Sun, 29 Jan 2017 13:32:57: 4000000
INFO @ Sun, 29 Jan 2017 13:32:59: 5000000
INFO @ Sun, 29 Jan 2017 13:33:01: 6000000
INFO @ Sun, 29 Jan 2017 13:33:02: 7000000
INFO @ Sun, 29 Jan 2017 13:33:04: 8000000
INFO @ Sun, 29 Jan 2017 13:33:06: 9000000
INFO @ Sun, 29 Jan 2017 13:33:07: 10000000
INFO @ Sun, 29 Jan 2017 13:33:09: 11000000
INFO @ Sun, 29 Jan 2017 13:33:10: 12000000
INFO @ Sun, 29 Jan 2017 13:33:12: 13000000
INFO @ Sun, 29 Jan 2017 13:33:13: 14000000
INFO @ Sun, 29 Jan 2017 13:33:15: 15000000
INFO @ Sun, 29 Jan 2017 13:33:16: 16000000
INFO @ Sun, 29 Jan 2017 13:33:18: 17000000
INFO @ Sun, 29 Jan 2017 13:33:19: 18000000
INFO @ Sun, 29 Jan 2017 13:33:21: 19000000
INFO @ Sun, 29 Jan 2017 13:33:23: 20000000
INFO @ Sun, 29 Jan 2017 13:33:24: 21000000
INFO @ Sun, 29 Jan 2017 13:33:26: 22000000
INFO @ Sun, 29 Jan 2017 13:33:28: 23000000
INFO @ Sun, 29 Jan 2017 13:33:30: 24000000
INFO @ Sun, 29 Jan 2017 13:33:31: 25000000
INFO @ Sun, 29 Jan 2017 13:33:33: 26000000
INFO @ Sun, 29 Jan 2017 13:33:34: 27000000
INFO @ Sun, 29 Jan 2017 13:33:36: 28000000
INFO @ Sun, 29 Jan 2017 13:33:37: 29000000
INFO @ Sun, 29 Jan 2017 13:33:39: 30000000
INFO @ Sun, 29 Jan 2017 13:33:41: 31000000
INFO @ Sun, 29 Jan 2017 13:33:43: 32000000
INFO @ Sun, 29 Jan 2017 13:33:44: 33000000
INFO @ Sun, 29 Jan 2017 13:33:46: 34000000
INFO @ Sun, 29 Jan 2017 13:33:48: 35000000
INFO @ Sun, 29 Jan 2017 13:33:52: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:33:53: 1000000
INFO @ Sun, 29 Jan 2017 13:33:55: 2000000
INFO @ Sun, 29 Jan 2017 13:33:56: 3000000
INFO @ Sun, 29 Jan 2017 13:33:58: 4000000
INFO @ Sun, 29 Jan 2017 13:33:59: 5000000
INFO @ Sun, 29 Jan 2017 13:34:00: 6000000
INFO @ Sun, 29 Jan 2017 13:34:02: 7000000
INFO @ Sun, 29 Jan 2017 13:34:04: 8000000
INFO @ Sun, 29 Jan 2017 13:34:05: 9000000
INFO @ Sun, 29 Jan 2017 13:34:06: 10000000
INFO @ Sun, 29 Jan 2017 13:34:08: 11000000
INFO @ Sun, 29 Jan 2017 13:34:09: 12000000
INFO @ Sun, 29 Jan 2017 13:34:10: 13000000
INFO @ Sun, 29 Jan 2017 13:34:12: 14000000
INFO @ Sun, 29 Jan 2017 13:34:13: 15000000
INFO @ Sun, 29 Jan 2017 13:34:15: 16000000
INFO @ Sun, 29 Jan 2017 13:34:16: 17000000
INFO @ Sun, 29 Jan 2017 13:34:18: 18000000
INFO @ Sun, 29 Jan 2017 13:34:19: 19000000
INFO @ Sun, 29 Jan 2017 13:34:21: 20000000
INFO @ Sun, 29 Jan 2017 13:34:22: 21000000
INFO @ Sun, 29 Jan 2017 13:34:23: 22000000
INFO @ Sun, 29 Jan 2017 13:34:25: 23000000
INFO @ Sun, 29 Jan 2017 13:34:26: 24000000
INFO @ Sun, 29 Jan 2017 13:34:28: 25000000
INFO @ Sun, 29 Jan 2017 13:34:29: 26000000
INFO @ Sun, 29 Jan 2017 13:34:31: 27000000
INFO @ Sun, 29 Jan 2017 13:34:33: 28000000
INFO @ Sun, 29 Jan 2017 13:34:34: 29000000
INFO @ Sun, 29 Jan 2017 13:34:35: 30000000
INFO @ Sun, 29 Jan 2017 13:34:37: 31000000
INFO @ Sun, 29 Jan 2017 13:34:38: 32000000
INFO @ Sun, 29 Jan 2017 13:34:39: 33000000
INFO @ Sun, 29 Jan 2017 13:34:41: 34000000
INFO @ Sun, 29 Jan 2017 13:34:42: 35000000
INFO @ Sun, 29 Jan 2017 13:34:44: 36000000
INFO @ Sun, 29 Jan 2017 13:34:45: 37000000
INFO @ Sun, 29 Jan 2017 13:34:46: 38000000
INFO @ Sun, 29 Jan 2017 13:34:48: 39000000
INFO @ Sun, 29 Jan 2017 13:34:49: 40000000
INFO @ Sun, 29 Jan 2017 13:34:51: 41000000
INFO @ Sun, 29 Jan 2017 13:34:52: 42000000
INFO @ Sun, 29 Jan 2017 13:34:54: 43000000
INFO @ Sun, 29 Jan 2017 13:34:55: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:34:55: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:34:55: #1 total tags in treatment: 35775777
INFO @ Sun, 29 Jan 2017 13:34:55: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:34:55: #1 finished!
INFO @ Sun, 29 Jan 2017 13:34:55: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:34:55: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:34:55: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:34:55: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:34:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 13:34:55: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:38:53: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:41:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:41:57: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 13:41:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 13:42:00: Done!
|
| Num | 30 | | ID | task.callpeak_macs2.macs2_ppr2.line_71.id_39 | | Name | macs2 ppr2 | | Thread | thread_Root | | PID | 36094 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:19:02 | | End | 2017-01-29 13:41:10 | | Elapsed | 00:22:07 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
32727 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 13:19:23:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 265 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 13:19:23: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:19:23: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:19:25: 1000000
INFO @ Sun, 29 Jan 2017 13:19:26: 2000000
INFO @ Sun, 29 Jan 2017 13:19:28: 3000000
INFO @ Sun, 29 Jan 2017 13:19:29: 4000000
INFO @ Sun, 29 Jan 2017 13:19:31: 5000000
INFO @ Sun, 29 Jan 2017 13:19:32: 6000000
INFO @ Sun, 29 Jan 2017 13:19:34: 7000000
INFO @ Sun, 29 Jan 2017 13:19:36: 8000000
INFO @ Sun, 29 Jan 2017 13:19:37: 9000000
INFO @ Sun, 29 Jan 2017 13:19:39: 10000000
INFO @ Sun, 29 Jan 2017 13:19:40: 11000000
INFO @ Sun, 29 Jan 2017 13:19:42: 12000000
INFO @ Sun, 29 Jan 2017 13:19:43: 13000000
INFO @ Sun, 29 Jan 2017 13:19:45: 14000000
INFO @ Sun, 29 Jan 2017 13:19:46: 15000000
INFO @ Sun, 29 Jan 2017 13:19:48: 16000000
INFO @ Sun, 29 Jan 2017 13:19:49: 17000000
INFO @ Sun, 29 Jan 2017 13:19:51: 18000000
INFO @ Sun, 29 Jan 2017 13:19:52: 19000000
INFO @ Sun, 29 Jan 2017 13:19:54: 20000000
INFO @ Sun, 29 Jan 2017 13:19:55: 21000000
INFO @ Sun, 29 Jan 2017 13:19:57: 22000000
INFO @ Sun, 29 Jan 2017 13:19:58: 23000000
INFO @ Sun, 29 Jan 2017 13:20:00: 24000000
INFO @ Sun, 29 Jan 2017 13:20:01: 25000000
INFO @ Sun, 29 Jan 2017 13:20:03: 26000000
INFO @ Sun, 29 Jan 2017 13:20:04: 27000000
INFO @ Sun, 29 Jan 2017 13:20:06: 28000000
INFO @ Sun, 29 Jan 2017 13:20:07: 29000000
INFO @ Sun, 29 Jan 2017 13:20:09: 30000000
INFO @ Sun, 29 Jan 2017 13:20:10: 31000000
INFO @ Sun, 29 Jan 2017 13:20:12: 32000000
INFO @ Sun, 29 Jan 2017 13:20:13: 33000000
INFO @ Sun, 29 Jan 2017 13:20:15: 34000000
INFO @ Sun, 29 Jan 2017 13:20:16: 35000000
INFO @ Sun, 29 Jan 2017 13:20:20: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:20:21: 1000000
INFO @ Sun, 29 Jan 2017 13:20:23: 2000000
INFO @ Sun, 29 Jan 2017 13:20:24: 3000000
INFO @ Sun, 29 Jan 2017 13:20:25: 4000000
INFO @ Sun, 29 Jan 2017 13:20:27: 5000000
INFO @ Sun, 29 Jan 2017 13:20:28: 6000000
INFO @ Sun, 29 Jan 2017 13:20:29: 7000000
INFO @ Sun, 29 Jan 2017 13:20:31: 8000000
INFO @ Sun, 29 Jan 2017 13:20:32: 9000000
INFO @ Sun, 29 Jan 2017 13:20:34: 10000000
INFO @ Sun, 29 Jan 2017 13:20:35: 11000000
INFO @ Sun, 29 Jan 2017 13:20:36: 12000000
INFO @ Sun, 29 Jan 2017 13:20:38: 13000000
INFO @ Sun, 29 Jan 2017 13:20:39: 14000000
INFO @ Sun, 29 Jan 2017 13:20:40: 15000000
INFO @ Sun, 29 Jan 2017 13:20:42: 16000000
INFO @ Sun, 29 Jan 2017 13:20:43: 17000000
INFO @ Sun, 29 Jan 2017 13:20:45: 18000000
INFO @ Sun, 29 Jan 2017 13:20:46: 19000000
INFO @ Sun, 29 Jan 2017 13:20:47: 20000000
INFO @ Sun, 29 Jan 2017 13:20:49: 21000000
INFO @ Sun, 29 Jan 2017 13:20:50: 22000000
INFO @ Sun, 29 Jan 2017 13:20:52: 23000000
INFO @ Sun, 29 Jan 2017 13:20:53: 24000000
INFO @ Sun, 29 Jan 2017 13:20:54: 25000000
INFO @ Sun, 29 Jan 2017 13:20:56: 26000000
INFO @ Sun, 29 Jan 2017 13:20:57: 27000000
INFO @ Sun, 29 Jan 2017 13:20:58: 28000000
INFO @ Sun, 29 Jan 2017 13:21:00: 29000000
INFO @ Sun, 29 Jan 2017 13:21:01: 30000000
INFO @ Sun, 29 Jan 2017 13:21:02: 31000000
INFO @ Sun, 29 Jan 2017 13:21:04: 32000000
INFO @ Sun, 29 Jan 2017 13:21:05: 33000000
INFO @ Sun, 29 Jan 2017 13:21:07: 34000000
INFO @ Sun, 29 Jan 2017 13:21:08: 35000000
INFO @ Sun, 29 Jan 2017 13:21:09: 36000000
INFO @ Sun, 29 Jan 2017 13:21:11: 37000000
INFO @ Sun, 29 Jan 2017 13:21:12: 38000000
INFO @ Sun, 29 Jan 2017 13:21:13: 39000000
INFO @ Sun, 29 Jan 2017 13:21:15: 40000000
INFO @ Sun, 29 Jan 2017 13:21:16: 41000000
INFO @ Sun, 29 Jan 2017 13:21:18: 42000000
INFO @ Sun, 29 Jan 2017 13:21:19: 43000000
INFO @ Sun, 29 Jan 2017 13:21:20: #1 tag size is determined as 49 bps
INFO @ Sun, 29 Jan 2017 13:21:20: #1 tag size = 49
INFO @ Sun, 29 Jan 2017 13:21:20: #1 total tags in treatment: 35775777
INFO @ Sun, 29 Jan 2017 13:21:20: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:21:20: #1 finished!
INFO @ Sun, 29 Jan 2017 13:21:20: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:21:20: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:21:20: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:21:20: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:21:20: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 13:21:20: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:25:15: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 13:25:15: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 13:25:15: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 13:25:15: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 13:25:15: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:31:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:31:51: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 13:31:52: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 13:31:53: Done!
INFO @ Sun, 29 Jan 2017 13:31:56:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 13:31:56: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:31:56: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:31:57: 1000000
INFO @ Sun, 29 Jan 2017 13:31:59: 2000000
INFO @ Sun, 29 Jan 2017 13:32:01: 3000000
INFO @ Sun, 29 Jan 2017 13:32:02: 4000000
INFO @ Sun, 29 Jan 2017 13:32:04: 5000000
INFO @ Sun, 29 Jan 2017 13:32:05: 6000000
INFO @ Sun, 29 Jan 2017 13:32:07: 7000000
INFO @ Sun, 29 Jan 2017 13:32:08: 8000000
INFO @ Sun, 29 Jan 2017 13:32:10: 9000000
INFO @ Sun, 29 Jan 2017 13:32:11: 10000000
INFO @ Sun, 29 Jan 2017 13:32:13: 11000000
INFO @ Sun, 29 Jan 2017 13:32:14: 12000000
INFO @ Sun, 29 Jan 2017 13:32:16: 13000000
INFO @ Sun, 29 Jan 2017 13:32:17: 14000000
INFO @ Sun, 29 Jan 2017 13:32:19: 15000000
INFO @ Sun, 29 Jan 2017 13:32:20: 16000000
INFO @ Sun, 29 Jan 2017 13:32:22: 17000000
INFO @ Sun, 29 Jan 2017 13:32:23: 18000000
INFO @ Sun, 29 Jan 2017 13:32:25: 19000000
INFO @ Sun, 29 Jan 2017 13:32:26: 20000000
INFO @ Sun, 29 Jan 2017 13:32:28: 21000000
INFO @ Sun, 29 Jan 2017 13:32:30: 22000000
INFO @ Sun, 29 Jan 2017 13:32:31: 23000000
INFO @ Sun, 29 Jan 2017 13:32:33: 24000000
INFO @ Sun, 29 Jan 2017 13:32:34: 25000000
INFO @ Sun, 29 Jan 2017 13:32:36: 26000000
INFO @ Sun, 29 Jan 2017 13:32:37: 27000000
INFO @ Sun, 29 Jan 2017 13:32:39: 28000000
INFO @ Sun, 29 Jan 2017 13:32:40: 29000000
INFO @ Sun, 29 Jan 2017 13:32:42: 30000000
INFO @ Sun, 29 Jan 2017 13:32:43: 31000000
INFO @ Sun, 29 Jan 2017 13:32:45: 32000000
INFO @ Sun, 29 Jan 2017 13:32:46: 33000000
INFO @ Sun, 29 Jan 2017 13:32:48: 34000000
INFO @ Sun, 29 Jan 2017 13:32:49: 35000000
INFO @ Sun, 29 Jan 2017 13:32:53: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:32:54: 1000000
INFO @ Sun, 29 Jan 2017 13:32:56: 2000000
INFO @ Sun, 29 Jan 2017 13:32:57: 3000000
INFO @ Sun, 29 Jan 2017 13:32:58: 4000000
INFO @ Sun, 29 Jan 2017 13:33:00: 5000000
INFO @ Sun, 29 Jan 2017 13:33:01: 6000000
INFO @ Sun, 29 Jan 2017 13:33:03: 7000000
INFO @ Sun, 29 Jan 2017 13:33:04: 8000000
INFO @ Sun, 29 Jan 2017 13:33:05: 9000000
INFO @ Sun, 29 Jan 2017 13:33:07: 10000000
INFO @ Sun, 29 Jan 2017 13:33:08: 11000000
INFO @ Sun, 29 Jan 2017 13:33:09: 12000000
INFO @ Sun, 29 Jan 2017 13:33:11: 13000000
INFO @ Sun, 29 Jan 2017 13:33:12: 14000000
INFO @ Sun, 29 Jan 2017 13:33:14: 15000000
INFO @ Sun, 29 Jan 2017 13:33:15: 16000000
INFO @ Sun, 29 Jan 2017 13:33:16: 17000000
INFO @ Sun, 29 Jan 2017 13:33:18: 18000000
INFO @ Sun, 29 Jan 2017 13:33:19: 19000000
INFO @ Sun, 29 Jan 2017 13:33:21: 20000000
INFO @ Sun, 29 Jan 2017 13:33:22: 21000000
INFO @ Sun, 29 Jan 2017 13:33:23: 22000000
INFO @ Sun, 29 Jan 2017 13:33:25: 23000000
INFO @ Sun, 29 Jan 2017 13:33:26: 24000000
INFO @ Sun, 29 Jan 2017 13:33:28: 25000000
INFO @ Sun, 29 Jan 2017 13:33:29: 26000000
INFO @ Sun, 29 Jan 2017 13:33:30: 27000000
INFO @ Sun, 29 Jan 2017 13:33:32: 28000000
INFO @ Sun, 29 Jan 2017 13:33:33: 29000000
INFO @ Sun, 29 Jan 2017 13:33:35: 30000000
INFO @ Sun, 29 Jan 2017 13:33:36: 31000000
INFO @ Sun, 29 Jan 2017 13:33:37: 32000000
INFO @ Sun, 29 Jan 2017 13:33:39: 33000000
INFO @ Sun, 29 Jan 2017 13:33:40: 34000000
INFO @ Sun, 29 Jan 2017 13:33:42: 35000000
INFO @ Sun, 29 Jan 2017 13:33:43: 36000000
INFO @ Sun, 29 Jan 2017 13:33:44: 37000000
INFO @ Sun, 29 Jan 2017 13:33:46: 38000000
INFO @ Sun, 29 Jan 2017 13:33:47: 39000000
INFO @ Sun, 29 Jan 2017 13:33:49: 40000000
INFO @ Sun, 29 Jan 2017 13:33:50: 41000000
INFO @ Sun, 29 Jan 2017 13:33:51: 42000000
INFO @ Sun, 29 Jan 2017 13:33:53: 43000000
INFO @ Sun, 29 Jan 2017 13:33:54: #1 tag size is determined as 49 bps
INFO @ Sun, 29 Jan 2017 13:33:54: #1 tag size = 49
INFO @ Sun, 29 Jan 2017 13:33:54: #1 total tags in treatment: 35775777
INFO @ Sun, 29 Jan 2017 13:33:54: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:33:54: #1 finished!
INFO @ Sun, 29 Jan 2017 13:33:54: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:33:54: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:33:54: #2 Use 265 as fragment length
INFO @ Sun, 29 Jan 2017 13:33:54: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:33:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 13:33:54: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:37:35: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:41:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:41:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 13:41:03: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 13:41:04: Done!
|
| Num | 31 | | ID | task.callpeak_macs2.macs2_rep1.line_71.id_40 | | Name | macs2 rep1 | | Thread | thread_Root | | PID | 36095 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:19:03 | | End | 2017-01-29 14:25:45 | | Elapsed | 01:06:42 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1 -o "SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1 -o "SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
13084 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 13:19:24:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 255 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 13:19:24: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:19:24: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:19:26: 1000000
INFO @ Sun, 29 Jan 2017 13:19:27: 2000000
INFO @ Sun, 29 Jan 2017 13:19:29: 3000000
INFO @ Sun, 29 Jan 2017 13:19:30: 4000000
INFO @ Sun, 29 Jan 2017 13:19:31: 5000000
INFO @ Sun, 29 Jan 2017 13:19:33: 6000000
INFO @ Sun, 29 Jan 2017 13:19:34: 7000000
INFO @ Sun, 29 Jan 2017 13:19:35: 8000000
INFO @ Sun, 29 Jan 2017 13:19:37: 9000000
INFO @ Sun, 29 Jan 2017 13:19:38: 10000000
INFO @ Sun, 29 Jan 2017 13:19:39: 11000000
INFO @ Sun, 29 Jan 2017 13:19:40: 12000000
INFO @ Sun, 29 Jan 2017 13:19:42: 13000000
INFO @ Sun, 29 Jan 2017 13:19:43: 14000000
INFO @ Sun, 29 Jan 2017 13:19:44: 15000000
INFO @ Sun, 29 Jan 2017 13:19:46: 16000000
INFO @ Sun, 29 Jan 2017 13:19:47: 17000000
INFO @ Sun, 29 Jan 2017 13:19:48: 18000000
INFO @ Sun, 29 Jan 2017 13:19:50: 19000000
INFO @ Sun, 29 Jan 2017 13:19:51: 20000000
INFO @ Sun, 29 Jan 2017 13:19:52: 21000000
INFO @ Sun, 29 Jan 2017 13:19:54: 22000000
INFO @ Sun, 29 Jan 2017 13:19:55: 23000000
INFO @ Sun, 29 Jan 2017 13:19:56: 24000000
INFO @ Sun, 29 Jan 2017 13:19:58: 25000000
INFO @ Sun, 29 Jan 2017 13:19:59: 26000000
INFO @ Sun, 29 Jan 2017 13:20:00: 27000000
INFO @ Sun, 29 Jan 2017 13:20:02: 28000000
INFO @ Sun, 29 Jan 2017 13:20:03: 29000000
INFO @ Sun, 29 Jan 2017 13:20:04: 30000000
INFO @ Sun, 29 Jan 2017 13:20:06: 31000000
INFO @ Sun, 29 Jan 2017 13:20:07: 32000000
INFO @ Sun, 29 Jan 2017 13:20:08: 33000000
INFO @ Sun, 29 Jan 2017 13:20:10: 34000000
INFO @ Sun, 29 Jan 2017 13:20:11: 35000000
INFO @ Sun, 29 Jan 2017 13:20:12: 36000000
INFO @ Sun, 29 Jan 2017 13:20:14: 37000000
INFO @ Sun, 29 Jan 2017 13:20:15: 38000000
INFO @ Sun, 29 Jan 2017 13:20:16: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:20:17: 1000000
INFO @ Sun, 29 Jan 2017 13:20:18: 2000000
INFO @ Sun, 29 Jan 2017 13:20:20: 3000000
INFO @ Sun, 29 Jan 2017 13:20:21: 4000000
INFO @ Sun, 29 Jan 2017 13:20:23: 5000000
INFO @ Sun, 29 Jan 2017 13:20:24: 6000000
INFO @ Sun, 29 Jan 2017 13:20:25: 7000000
INFO @ Sun, 29 Jan 2017 13:20:27: 8000000
INFO @ Sun, 29 Jan 2017 13:20:28: 9000000
INFO @ Sun, 29 Jan 2017 13:20:29: 10000000
INFO @ Sun, 29 Jan 2017 13:20:31: 11000000
INFO @ Sun, 29 Jan 2017 13:20:32: 12000000
INFO @ Sun, 29 Jan 2017 13:20:33: 13000000
INFO @ Sun, 29 Jan 2017 13:20:34: 14000000
INFO @ Sun, 29 Jan 2017 13:20:36: 15000000
INFO @ Sun, 29 Jan 2017 13:20:37: 16000000
INFO @ Sun, 29 Jan 2017 13:20:38: 17000000
INFO @ Sun, 29 Jan 2017 13:20:40: 18000000
INFO @ Sun, 29 Jan 2017 13:20:41: 19000000
INFO @ Sun, 29 Jan 2017 13:20:42: 20000000
INFO @ Sun, 29 Jan 2017 13:20:44: 21000000
INFO @ Sun, 29 Jan 2017 13:20:45: 22000000
INFO @ Sun, 29 Jan 2017 13:20:46: 23000000
INFO @ Sun, 29 Jan 2017 13:20:48: 24000000
INFO @ Sun, 29 Jan 2017 13:20:49: 25000000
INFO @ Sun, 29 Jan 2017 13:20:50: 26000000
INFO @ Sun, 29 Jan 2017 13:20:52: 27000000
INFO @ Sun, 29 Jan 2017 13:20:53: 28000000
INFO @ Sun, 29 Jan 2017 13:20:54: 29000000
INFO @ Sun, 29 Jan 2017 13:20:55: 30000000
INFO @ Sun, 29 Jan 2017 13:20:57: 31000000
INFO @ Sun, 29 Jan 2017 13:20:58: 32000000
INFO @ Sun, 29 Jan 2017 13:20:59: 33000000
INFO @ Sun, 29 Jan 2017 13:21:01: 34000000
INFO @ Sun, 29 Jan 2017 13:21:02: 35000000
INFO @ Sun, 29 Jan 2017 13:21:03: 36000000
INFO @ Sun, 29 Jan 2017 13:21:04: 37000000
INFO @ Sun, 29 Jan 2017 13:21:06: 38000000
INFO @ Sun, 29 Jan 2017 13:21:07: 39000000
INFO @ Sun, 29 Jan 2017 13:21:08: 40000000
INFO @ Sun, 29 Jan 2017 13:21:10: 41000000
INFO @ Sun, 29 Jan 2017 13:21:11: 42000000
INFO @ Sun, 29 Jan 2017 13:21:13: 43000000
INFO @ Sun, 29 Jan 2017 13:21:14: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:21:14: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:21:14: #1 total tags in treatment: 38042012
INFO @ Sun, 29 Jan 2017 13:21:14: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:21:14: #1 finished!
INFO @ Sun, 29 Jan 2017 13:21:14: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:21:14: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:21:14: #2 Use 255 as fragment length
INFO @ Sun, 29 Jan 2017 13:21:14: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:21:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 13:21:14: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:24:57: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 13:24:57: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 13:24:57: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 13:24:57: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 13:24:57: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:31:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:31:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 13:31:27: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 13:31:28: Done!
INFO @ Sun, 29 Jan 2017 13:31:33:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep1/SRR1946778.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 13:31:33: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:31:33: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:31:34: 1000000
INFO @ Sun, 29 Jan 2017 13:31:36: 2000000
INFO @ Sun, 29 Jan 2017 13:31:37: 3000000
INFO @ Sun, 29 Jan 2017 13:31:39: 4000000
INFO @ Sun, 29 Jan 2017 13:31:40: 5000000
INFO @ Sun, 29 Jan 2017 13:31:42: 6000000
INFO @ Sun, 29 Jan 2017 13:31:43: 7000000
INFO @ Sun, 29 Jan 2017 13:31:44: 8000000
INFO @ Sun, 29 Jan 2017 13:31:46: 9000000
INFO @ Sun, 29 Jan 2017 13:31:47: 10000000
INFO @ Sun, 29 Jan 2017 13:31:49: 11000000
INFO @ Sun, 29 Jan 2017 13:31:51: 12000000
INFO @ Sun, 29 Jan 2017 13:31:53: 13000000
INFO @ Sun, 29 Jan 2017 13:31:54: 14000000
INFO @ Sun, 29 Jan 2017 13:31:56: 15000000
INFO @ Sun, 29 Jan 2017 13:31:57: 16000000
INFO @ Sun, 29 Jan 2017 13:31:59: 17000000
INFO @ Sun, 29 Jan 2017 13:32:01: 18000000
INFO @ Sun, 29 Jan 2017 13:32:03: 19000000
INFO @ Sun, 29 Jan 2017 13:32:04: 20000000
INFO @ Sun, 29 Jan 2017 13:32:06: 21000000
INFO @ Sun, 29 Jan 2017 13:32:07: 22000000
INFO @ Sun, 29 Jan 2017 13:32:08: 23000000
INFO @ Sun, 29 Jan 2017 13:32:10: 24000000
INFO @ Sun, 29 Jan 2017 13:32:11: 25000000
INFO @ Sun, 29 Jan 2017 13:32:13: 26000000
INFO @ Sun, 29 Jan 2017 13:32:15: 27000000
INFO @ Sun, 29 Jan 2017 13:32:16: 28000000
INFO @ Sun, 29 Jan 2017 13:32:18: 29000000
INFO @ Sun, 29 Jan 2017 13:32:20: 30000000
INFO @ Sun, 29 Jan 2017 13:32:22: 31000000
INFO @ Sun, 29 Jan 2017 13:32:23: 32000000
INFO @ Sun, 29 Jan 2017 13:32:25: 33000000
INFO @ Sun, 29 Jan 2017 13:32:27: 34000000
INFO @ Sun, 29 Jan 2017 13:32:28: 35000000
INFO @ Sun, 29 Jan 2017 13:32:30: 36000000
INFO @ Sun, 29 Jan 2017 13:32:31: 37000000
INFO @ Sun, 29 Jan 2017 13:32:33: 38000000
INFO @ Sun, 29 Jan 2017 13:32:33: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:32:35: 1000000
INFO @ Sun, 29 Jan 2017 13:32:37: 2000000
INFO @ Sun, 29 Jan 2017 13:32:39: 3000000
INFO @ Sun, 29 Jan 2017 13:32:41: 4000000
INFO @ Sun, 29 Jan 2017 13:32:42: 5000000
INFO @ Sun, 29 Jan 2017 13:32:44: 6000000
INFO @ Sun, 29 Jan 2017 13:32:45: 7000000
INFO @ Sun, 29 Jan 2017 13:32:46: 8000000
INFO @ Sun, 29 Jan 2017 13:32:48: 9000000
INFO @ Sun, 29 Jan 2017 13:32:49: 10000000
INFO @ Sun, 29 Jan 2017 13:32:51: 11000000
INFO @ Sun, 29 Jan 2017 13:32:52: 12000000
INFO @ Sun, 29 Jan 2017 13:32:53: 13000000
INFO @ Sun, 29 Jan 2017 13:32:55: 14000000
INFO @ Sun, 29 Jan 2017 13:32:56: 15000000
INFO @ Sun, 29 Jan 2017 13:32:58: 16000000
INFO @ Sun, 29 Jan 2017 13:32:59: 17000000
INFO @ Sun, 29 Jan 2017 13:33:01: 18000000
INFO @ Sun, 29 Jan 2017 13:33:02: 19000000
INFO @ Sun, 29 Jan 2017 13:33:04: 20000000
INFO @ Sun, 29 Jan 2017 13:33:05: 21000000
INFO @ Sun, 29 Jan 2017 13:33:07: 22000000
INFO @ Sun, 29 Jan 2017 13:33:08: 23000000
INFO @ Sun, 29 Jan 2017 13:33:09: 24000000
INFO @ Sun, 29 Jan 2017 13:33:11: 25000000
INFO @ Sun, 29 Jan 2017 13:33:12: 26000000
INFO @ Sun, 29 Jan 2017 13:33:14: 27000000
INFO @ Sun, 29 Jan 2017 13:33:15: 28000000
INFO @ Sun, 29 Jan 2017 13:33:17: 29000000
INFO @ Sun, 29 Jan 2017 13:33:18: 30000000
INFO @ Sun, 29 Jan 2017 13:33:20: 31000000
INFO @ Sun, 29 Jan 2017 13:33:21: 32000000
INFO @ Sun, 29 Jan 2017 13:33:22: 33000000
INFO @ Sun, 29 Jan 2017 13:33:24: 34000000
INFO @ Sun, 29 Jan 2017 13:33:25: 35000000
INFO @ Sun, 29 Jan 2017 13:33:27: 36000000
INFO @ Sun, 29 Jan 2017 13:33:28: 37000000
INFO @ Sun, 29 Jan 2017 13:33:29: 38000000
INFO @ Sun, 29 Jan 2017 13:33:31: 39000000
INFO @ Sun, 29 Jan 2017 13:33:32: 40000000
INFO @ Sun, 29 Jan 2017 13:33:34: 41000000
INFO @ Sun, 29 Jan 2017 13:33:35: 42000000
INFO @ Sun, 29 Jan 2017 13:33:36: 43000000
INFO @ Sun, 29 Jan 2017 13:33:38: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:33:38: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:33:38: #1 total tags in treatment: 38042012
INFO @ Sun, 29 Jan 2017 13:33:38: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:33:38: #1 finished!
INFO @ Sun, 29 Jan 2017 13:33:38: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:33:38: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:33:38: #2 Use 255 as fragment length
INFO @ Sun, 29 Jan 2017 13:33:38: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:33:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 13:33:38: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:37:32: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:40:48: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:40:50: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 13:40:51: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 13:40:52: Done!
INFO @ Sun, 29 Jan 2017 13:40:59: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 13:42:23: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 13:43:53: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 13:44:52: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 29 Jan 2017 13:50:25: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 13:54:35: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_FE.bdg'!
INFO @ Sun, 29 Jan 2017 14:05:29: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 14:06:38: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 14:08:09: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 14:08:59: Values in your input bedGraph files will be multiplied by 38.042012 ...
INFO @ Sun, 29 Jan 2017 14:15:16: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Sun, 29 Jan 2017 14:15:59: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 14:18:40: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_ppois.bdg'!
|
| Num | 32 | | ID | task.callpeak_macs2.macs2_rep2.line_71.id_41 | | Name | macs2 rep2 | | Thread | thread_Root | | PID | 36096 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 13:41:12 | | End | 2017-01-29 14:46:16 | | Elapsed | 01:05:03 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
| | Dependencies | | |
# SYS command. line 73
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 74
export LC_COLLATE=C
# SYS command. line 79
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 275 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 275 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
exit; \
fi
# SYS command. line 121
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2 -o "SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2 -o "SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 153
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
49697 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 13:41:22:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 275 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
INFO @ Sun, 29 Jan 2017 13:41:22: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:41:22: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:41:24: 1000000
INFO @ Sun, 29 Jan 2017 13:41:25: 2000000
INFO @ Sun, 29 Jan 2017 13:41:27: 3000000
INFO @ Sun, 29 Jan 2017 13:41:28: 4000000
INFO @ Sun, 29 Jan 2017 13:41:29: 5000000
INFO @ Sun, 29 Jan 2017 13:41:31: 6000000
INFO @ Sun, 29 Jan 2017 13:41:32: 7000000
INFO @ Sun, 29 Jan 2017 13:41:33: 8000000
INFO @ Sun, 29 Jan 2017 13:41:35: 9000000
INFO @ Sun, 29 Jan 2017 13:41:36: 10000000
INFO @ Sun, 29 Jan 2017 13:41:38: 11000000
INFO @ Sun, 29 Jan 2017 13:41:39: 12000000
INFO @ Sun, 29 Jan 2017 13:41:40: 13000000
INFO @ Sun, 29 Jan 2017 13:41:42: 14000000
INFO @ Sun, 29 Jan 2017 13:41:43: 15000000
INFO @ Sun, 29 Jan 2017 13:41:44: 16000000
INFO @ Sun, 29 Jan 2017 13:41:46: 17000000
INFO @ Sun, 29 Jan 2017 13:41:47: 18000000
INFO @ Sun, 29 Jan 2017 13:41:49: 19000000
INFO @ Sun, 29 Jan 2017 13:41:50: 20000000
INFO @ Sun, 29 Jan 2017 13:41:51: 21000000
INFO @ Sun, 29 Jan 2017 13:41:53: 22000000
INFO @ Sun, 29 Jan 2017 13:41:54: 23000000
INFO @ Sun, 29 Jan 2017 13:41:56: 24000000
INFO @ Sun, 29 Jan 2017 13:41:57: 25000000
INFO @ Sun, 29 Jan 2017 13:41:58: 26000000
INFO @ Sun, 29 Jan 2017 13:42:00: 27000000
INFO @ Sun, 29 Jan 2017 13:42:01: 28000000
INFO @ Sun, 29 Jan 2017 13:42:02: 29000000
INFO @ Sun, 29 Jan 2017 13:42:04: 30000000
INFO @ Sun, 29 Jan 2017 13:42:05: 31000000
INFO @ Sun, 29 Jan 2017 13:42:07: 32000000
INFO @ Sun, 29 Jan 2017 13:42:08: 33000000
INFO @ Sun, 29 Jan 2017 13:42:09: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:42:10: 1000000
INFO @ Sun, 29 Jan 2017 13:42:12: 2000000
INFO @ Sun, 29 Jan 2017 13:42:13: 3000000
INFO @ Sun, 29 Jan 2017 13:42:15: 4000000
INFO @ Sun, 29 Jan 2017 13:42:16: 5000000
INFO @ Sun, 29 Jan 2017 13:42:17: 6000000
INFO @ Sun, 29 Jan 2017 13:42:19: 7000000
INFO @ Sun, 29 Jan 2017 13:42:20: 8000000
INFO @ Sun, 29 Jan 2017 13:42:21: 9000000
INFO @ Sun, 29 Jan 2017 13:42:23: 10000000
INFO @ Sun, 29 Jan 2017 13:42:24: 11000000
INFO @ Sun, 29 Jan 2017 13:42:25: 12000000
INFO @ Sun, 29 Jan 2017 13:42:27: 13000000
INFO @ Sun, 29 Jan 2017 13:42:28: 14000000
INFO @ Sun, 29 Jan 2017 13:42:30: 15000000
INFO @ Sun, 29 Jan 2017 13:42:31: 16000000
INFO @ Sun, 29 Jan 2017 13:42:32: 17000000
INFO @ Sun, 29 Jan 2017 13:42:34: 18000000
INFO @ Sun, 29 Jan 2017 13:42:35: 19000000
INFO @ Sun, 29 Jan 2017 13:42:36: 20000000
INFO @ Sun, 29 Jan 2017 13:42:38: 21000000
INFO @ Sun, 29 Jan 2017 13:42:39: 22000000
INFO @ Sun, 29 Jan 2017 13:42:41: 23000000
INFO @ Sun, 29 Jan 2017 13:42:42: 24000000
INFO @ Sun, 29 Jan 2017 13:42:43: 25000000
INFO @ Sun, 29 Jan 2017 13:42:45: 26000000
INFO @ Sun, 29 Jan 2017 13:42:46: 27000000
INFO @ Sun, 29 Jan 2017 13:42:47: 28000000
INFO @ Sun, 29 Jan 2017 13:42:49: 29000000
INFO @ Sun, 29 Jan 2017 13:42:50: 30000000
INFO @ Sun, 29 Jan 2017 13:42:52: 31000000
INFO @ Sun, 29 Jan 2017 13:42:53: 32000000
INFO @ Sun, 29 Jan 2017 13:42:54: 33000000
INFO @ Sun, 29 Jan 2017 13:42:56: 34000000
INFO @ Sun, 29 Jan 2017 13:42:57: 35000000
INFO @ Sun, 29 Jan 2017 13:42:58: 36000000
INFO @ Sun, 29 Jan 2017 13:43:00: 37000000
INFO @ Sun, 29 Jan 2017 13:43:01: 38000000
INFO @ Sun, 29 Jan 2017 13:43:03: 39000000
INFO @ Sun, 29 Jan 2017 13:43:04: 40000000
INFO @ Sun, 29 Jan 2017 13:43:05: 41000000
INFO @ Sun, 29 Jan 2017 13:43:07: 42000000
INFO @ Sun, 29 Jan 2017 13:43:08: 43000000
INFO @ Sun, 29 Jan 2017 13:43:09: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:43:09: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:43:09: #1 total tags in treatment: 33509542
INFO @ Sun, 29 Jan 2017 13:43:09: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:43:09: #1 finished!
INFO @ Sun, 29 Jan 2017 13:43:09: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:43:09: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:43:09: #2 Use 275 as fragment length
INFO @ Sun, 29 Jan 2017 13:43:09: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:43:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 13:43:09: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:46:33: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 13:46:33: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 13:46:33: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 13:46:33: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 13:46:33: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 13:52:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 13:52:52: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 13:52:53: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 13:52:53: Done!
INFO @ Sun, 29 Jan 2017 13:52:58:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 275 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/rep2/SRR1946779.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/align/ctl1/SRR1946788.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
INFO @ Sun, 29 Jan 2017 13:52:58: #1 read tag files...
INFO @ Sun, 29 Jan 2017 13:52:58: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 13:52:59: 1000000
INFO @ Sun, 29 Jan 2017 13:53:00: 2000000
INFO @ Sun, 29 Jan 2017 13:53:02: 3000000
INFO @ Sun, 29 Jan 2017 13:53:03: 4000000
INFO @ Sun, 29 Jan 2017 13:53:05: 5000000
INFO @ Sun, 29 Jan 2017 13:53:06: 6000000
INFO @ Sun, 29 Jan 2017 13:53:07: 7000000
INFO @ Sun, 29 Jan 2017 13:53:09: 8000000
INFO @ Sun, 29 Jan 2017 13:53:10: 9000000
INFO @ Sun, 29 Jan 2017 13:53:12: 10000000
INFO @ Sun, 29 Jan 2017 13:53:13: 11000000
INFO @ Sun, 29 Jan 2017 13:53:14: 12000000
INFO @ Sun, 29 Jan 2017 13:53:16: 13000000
INFO @ Sun, 29 Jan 2017 13:53:17: 14000000
INFO @ Sun, 29 Jan 2017 13:53:19: 15000000
INFO @ Sun, 29 Jan 2017 13:53:20: 16000000
INFO @ Sun, 29 Jan 2017 13:53:21: 17000000
INFO @ Sun, 29 Jan 2017 13:53:23: 18000000
INFO @ Sun, 29 Jan 2017 13:53:24: 19000000
INFO @ Sun, 29 Jan 2017 13:53:26: 20000000
INFO @ Sun, 29 Jan 2017 13:53:27: 21000000
INFO @ Sun, 29 Jan 2017 13:53:28: 22000000
INFO @ Sun, 29 Jan 2017 13:53:30: 23000000
INFO @ Sun, 29 Jan 2017 13:53:31: 24000000
INFO @ Sun, 29 Jan 2017 13:53:32: 25000000
INFO @ Sun, 29 Jan 2017 13:53:34: 26000000
INFO @ Sun, 29 Jan 2017 13:53:35: 27000000
INFO @ Sun, 29 Jan 2017 13:53:37: 28000000
INFO @ Sun, 29 Jan 2017 13:53:38: 29000000
INFO @ Sun, 29 Jan 2017 13:53:40: 30000000
INFO @ Sun, 29 Jan 2017 13:53:41: 31000000
INFO @ Sun, 29 Jan 2017 13:53:42: 32000000
INFO @ Sun, 29 Jan 2017 13:53:44: 33000000
INFO @ Sun, 29 Jan 2017 13:53:45: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 13:53:46: 1000000
INFO @ Sun, 29 Jan 2017 13:53:48: 2000000
INFO @ Sun, 29 Jan 2017 13:53:49: 3000000
INFO @ Sun, 29 Jan 2017 13:53:50: 4000000
INFO @ Sun, 29 Jan 2017 13:53:52: 5000000
INFO @ Sun, 29 Jan 2017 13:53:53: 6000000
INFO @ Sun, 29 Jan 2017 13:53:55: 7000000
INFO @ Sun, 29 Jan 2017 13:53:56: 8000000
INFO @ Sun, 29 Jan 2017 13:53:57: 9000000
INFO @ Sun, 29 Jan 2017 13:53:59: 10000000
INFO @ Sun, 29 Jan 2017 13:54:00: 11000000
INFO @ Sun, 29 Jan 2017 13:54:01: 12000000
INFO @ Sun, 29 Jan 2017 13:54:03: 13000000
INFO @ Sun, 29 Jan 2017 13:54:04: 14000000
INFO @ Sun, 29 Jan 2017 13:54:06: 15000000
INFO @ Sun, 29 Jan 2017 13:54:07: 16000000
INFO @ Sun, 29 Jan 2017 13:54:08: 17000000
INFO @ Sun, 29 Jan 2017 13:54:10: 18000000
INFO @ Sun, 29 Jan 2017 13:54:11: 19000000
INFO @ Sun, 29 Jan 2017 13:54:12: 20000000
INFO @ Sun, 29 Jan 2017 13:54:14: 21000000
INFO @ Sun, 29 Jan 2017 13:54:15: 22000000
INFO @ Sun, 29 Jan 2017 13:54:17: 23000000
INFO @ Sun, 29 Jan 2017 13:54:18: 24000000
INFO @ Sun, 29 Jan 2017 13:54:19: 25000000
INFO @ Sun, 29 Jan 2017 13:54:21: 26000000
INFO @ Sun, 29 Jan 2017 13:54:22: 27000000
INFO @ Sun, 29 Jan 2017 13:54:23: 28000000
INFO @ Sun, 29 Jan 2017 13:54:25: 29000000
INFO @ Sun, 29 Jan 2017 13:54:26: 30000000
INFO @ Sun, 29 Jan 2017 13:54:28: 31000000
INFO @ Sun, 29 Jan 2017 13:54:29: 32000000
INFO @ Sun, 29 Jan 2017 13:54:30: 33000000
INFO @ Sun, 29 Jan 2017 13:54:32: 34000000
INFO @ Sun, 29 Jan 2017 13:54:33: 35000000
INFO @ Sun, 29 Jan 2017 13:54:34: 36000000
INFO @ Sun, 29 Jan 2017 13:54:36: 37000000
INFO @ Sun, 29 Jan 2017 13:54:37: 38000000
INFO @ Sun, 29 Jan 2017 13:54:38: 39000000
INFO @ Sun, 29 Jan 2017 13:54:40: 40000000
INFO @ Sun, 29 Jan 2017 13:54:41: 41000000
INFO @ Sun, 29 Jan 2017 13:54:43: 42000000
INFO @ Sun, 29 Jan 2017 13:54:44: 43000000
INFO @ Sun, 29 Jan 2017 13:54:45: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 13:54:45: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 13:54:45: #1 total tags in treatment: 33509542
INFO @ Sun, 29 Jan 2017 13:54:45: #1 total tags in control: 43655247
INFO @ Sun, 29 Jan 2017 13:54:45: #1 finished!
INFO @ Sun, 29 Jan 2017 13:54:45: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 13:54:45: #2 Skipped...
INFO @ Sun, 29 Jan 2017 13:54:45: #2 Use 275 as fragment length
INFO @ Sun, 29 Jan 2017 13:54:45: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 13:54:45: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 13:54:45: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 13:58:35: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 14:02:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 14:02:12: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 14:02:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 14:02:14: Done!
INFO @ Sun, 29 Jan 2017 14:02:19: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 14:03:24: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 14:05:00: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 14:06:11: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 29 Jan 2017 14:11:57: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 14:16:20: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_FE.bdg'!
INFO @ Sun, 29 Jan 2017 14:25:24: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 14:26:28: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 14:28:04: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 14:29:10: Values in your input bedGraph files will be multiplied by 33.509542 ...
INFO @ Sun, 29 Jan 2017 14:34:40: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Sun, 29 Jan 2017 14:35:31: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 14:38:33: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign_ppois.bdg'!
|
| Num | 33 | | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_42 | | Name | naive_overlap_thresh | | Thread | thread_Root | | PID | 36097 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:48:57 | | End | 2017-01-29 14:50:08 | | Elapsed | 00:01:11 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 148
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.narrowPeak.gz
# SYS command. line 151
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz
# SYS command. line 154
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.narrowPeak.gz
# SYS command. line 156
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS=" "} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
# SYS command. line 158
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.narrowPeak.gz
# SYS command. line 160
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
14021 (process ID) old priority 0, new priority 10
Waiting for 49 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 11498 16989 Peak_52 296 . 6.89971 29.69127 23.93284 2811
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 11498 16989 Peak_52 296 . 6.89971 29.69127 23.93284 2811
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000205.2 55934 56424 Peak_88 289 . 5.40164 28.99326 23.48577 240
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000205.2 55934 56424 Peak_88 289 . 5.40164 28.99326 23.48577 240
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 55917 56416 Peak_307 210 . 4.48826 21.02198 16.10680 258
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 55917 56416 Peak_307 210 . 4.48826 21.02198 16.10680 258
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000205.2 40830 44265 Peak_92 260 . 6.38070 26.08770 20.63924 1004
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000205.2 40830 44265 Peak_92 260 . 6.38070 26.08770 20.63924 1004
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1 135579 135855 Peak_35325 68 . 3.76821 6.83621 4.02278 116
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000195.1 135579 135855 Peak_35325 68 . 3.76821 6.83621 4.02278 116
|
| Num | 34 | | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_43 | | Name | naive_overlap_thresh | | Thread | thread_Root | | PID | 36098 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:48:58 | | End | 2017-01-29 14:50:22 | | Elapsed | 00:01:23 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 148
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.gappedPeak.gz
# SYS command. line 151
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz
# SYS command. line 154
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.gappedPeak.gz
# SYS command. line 156
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS=" "} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
# SYS command. line 158
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz
# SYS command. line 160
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
14135 (process ID) old priority 0, new priority 10
Waiting for 43 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 135814 136525 Peak_230 56 . 135814 136525 0 2 1,1 0,710 3.95058 8.50051 5.62267
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 135814 136525 Peak_230 56 . 135814 136525 0 2 1,1 0,710 3.95058 8.50051 5.62267
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 130160 130946 Peak_3424 26 . 130160 130946 0 2 1,1 0,785 2.05570 4.34704 2.69451
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 130160 130946 Peak_3424 26 . 130160 130946 0 2 1,1 0,785 2.05570 4.34704 2.69451
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1 123853 124567 Peak_1373 34 . 123853 124567 0 2 1,1 0,713 1.98146 5.17099 3.41865
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1 123853 124567 Peak_1373 34 . 123853 124567 0 2 1,1 0,713 1.98146 5.17099 3.41865
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 151589 153325 Peak_415 48 . 151589 153325 0 2 1,1 0,1735 2.56441 7.24461 4.88287
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 151589 153325 Peak_415 48 . 151589 153325 0 2 1,1 0,1735 2.56441 7.24461 4.88287
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1 123858 124562 Peak_3743 24 . 123858 124562 0 2 1,1 0,703 1.57069 3.84329 2.40510
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000195.1 123858 124562 Peak_3743 24 . 123858 124562 0 2 1,1 0,703 1.57069 3.84329 2.40510
|
| Num | 35 | | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_143.id_44 | | Name | naive_overlap_thresh | | Thread | thread_Root | | PID | 36099 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:48:59 | | End | 2017-01-29 14:50:22 | | Elapsed | 00:01:22 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
| | Dependencies | | |
# SYS command. line 145
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 148
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.broadPeak.gz
# SYS command. line 151
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz
# SYS command. line 154
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.broadPeak.gz
# SYS command. line 156
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[0-9XY]+(?!_)' | awk 'BEGIN{OFS=" "} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
# SYS command. line 158
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz
# SYS command. line 160
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
14136 (process ID) old priority 0, new priority 10
Waiting for 48 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 135814 136525 Peak_230 56 . 3.95058 8.50051 5.62267
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000205.2 135814 136525 Peak_230 56 . 3.95058 8.50051 5.62267
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 130160 130946 Peak_3424 26 . 2.05570 4.34704 2.69451
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 130160 130946 Peak_3424 26 . 2.05570 4.34704 2.69451
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1 123853 124567 Peak_1373 34 . 1.98146 5.17099 3.41865
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1 123853 124567 Peak_1373 34 . 1.98146 5.17099 3.41865
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 151589 153325 Peak_415 48 . 2.56441 7.24461 4.88287
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1 151589 153325 Peak_415 48 . 2.56441 7.24461 4.88287
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1 123858 124562 Peak_3743 24 . 1.57069 3.84329 2.40510
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000195.1 123858 124562 Peak_3743 24 . 1.57069 3.84329 2.40510
|
| Num | 36 | | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_pooled.line_27.id_45 | | Name | blacklist_filter peak_pooled | | Thread | thread_Root | | PID | 4529 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:50:23 | | End | 2017-01-29 14:51:32 | | Elapsed | 00:01:09 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 29
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 31
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
4533 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 40863 44265 Peak_163 244 . 5.90620 24.46986 19.36119 1868
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 40863 44265 Peak_163 244 . 5.90620 24.46986 19.36119 1868
|
| Num | 37 | | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_46 | | Name | blacklist_filter peak 1 | | Thread | thread_Root | | PID | 4641 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:50:25 | | End | 2017-01-29 14:51:33 | | Elapsed | 00:01:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 29
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 31
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
4650 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 11498 16989 Peak_52 296 . 6.89971 29.69127 23.93284 2811
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 11498 16989 Peak_52 296 . 6.89971 29.69127 23.93284 2811
|
| Num | 38 | | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_2.line_27.id_47 | | Name | blacklist_filter peak 2 | | Thread | thread_Root | | PID | 4706 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:50:26 | | End | 2017-01-29 14:51:34 | | Elapsed | 00:01:07 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 29
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 31
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
4711 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 55934 56424 Peak_88 289 . 5.40164 28.99326 23.48577 240
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000205.2 55934 56424 Peak_88 289 . 5.40164 28.99326 23.48577 240
|
| Num | 39 | | ID | task.report.peak2hammock.line_412.id_48 | | Name | peak2hammock | | Thread | thread_Root | | PID | 8922 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:51:35 | | End | 2017-01-29 14:51:45 | | Elapsed | 00:00:10 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
| | Dependencies | | |
# SYS command. line 414
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 415
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
# SYS command. line 417
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
--------------------Stdout--------------------
8926 (process ID) old priority 0, new priority 10
|
| Num | 40 | | ID | task.report.peak2hammock.line_412.id_49 | | Name | peak2hammock | | Thread | thread_Root | | PID | 9596 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:51:46 | | End | 2017-01-29 14:52:00 | | Elapsed | 00:00:13 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
| | Dependencies | | |
# SYS command. line 414
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 415
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
# SYS command. line 417
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
--------------------Stdout--------------------
9600 (process ID) old priority 0, new priority 10
|
| Num | 41 | | ID | task.graphviz.report.line_97.id_50 | | Name | report | | Thread | thread_Root | | PID | 10547 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:52:00 | | End | 2017-01-29 14:52:09 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | | | Output files | | | Dependencies | | |
# SYS command. line 98
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/report/H3K9me2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/report/H3K9me2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/report/H3K9me2_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
10552 (process ID) old priority 0, new priority 10
|
| Num | 42 | | ID | task.report.pdf2png.line_379.id_57 | | Name | pdf2png | | Thread | thread_Root | | PID | 10553 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:52:01 | | End | 2017-01-29 14:52:09 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.png
| | Dependencies | | |
# SYS command. line 380
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 381
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
10574 (process ID) old priority 0, new priority 10
|
| Num | 43 | | ID | task.report.pdf2png.line_379.id_58 | | Name | pdf2png | | Thread | thread_Root | | PID | 10558 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | | | Mem | | | | Start | 2017-01-29 14:52:01 | | End | 2017-01-29 14:52:09 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.png
| | Dependencies | | |
# SYS command. line 380
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 381
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Simon2015Data/H3K9me2/out/qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
10571 (process ID) old priority 0, new priority 10
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