| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_171027_380 |
| Start time | 2016-11-10 17:10:27 |
| Run time | 2 days 19:56:20.903 |
| Tasks executed | 4 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 bwa_sam rep1 |
| Arguments* | [-title, SRR1370897_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370897_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_41 | thread_Root | chipseq.bds.20161110_171027_380_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161110_171027_380_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 |
| thread_42 | thread_Root | chipseq.bds.20161110_171027_380_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161110_171027_380_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 110
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 113
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/HughesZnfData/RawReadsFiles/SRR1370897_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/rep1/SRR1370897_1.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 49356 (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] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.17 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.91 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.91 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.78 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.19 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.09 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.06 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.04 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.23 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.42 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.98 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.96 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... 29.64 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.68 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.20 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.63 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.49 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.55 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.17 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.39 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.86 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.71 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.67 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.41 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.93 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.58 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.56 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.45 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.51 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.01 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 24555168 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/HughesZnfData/RawReadsFiles/SRR1370897_1.fastq.gz [main] Real time: 3140.022 sec; CPU: 3133.924 sec | ||||||||||||||||||||||||||||||||||||||||
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# 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 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 12262 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
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# 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/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/qc/ctl1/ss_50M_2000_GRCh38.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-------------------- 19714 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 20:01:07 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/qc/ctl1/ss_50M_2000_GRCh38.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 [Thu Nov 10 20:01:07 PST 2016] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 20:01:30 MarkDuplicates Start of doWork freeMemory: 254877736; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 20:01:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 20:01:30 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 20:02:42 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 31s. Last read position: chr1:22,298,551 INFO 2016-11-10 20:02:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 31s. Last read position: chr1:41,895,424 INFO 2016-11-10 20:03:13 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:03:39 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 26s. Last read position: chr1:63,396,527 INFO 2016-11-10 20:03:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:04:10 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 30s. Last read position: chr1:89,147,707 INFO 2016-11-10 20:04:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:46 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 35s. Last read position: chr1:115,615,553 INFO 2016-11-10 20:04:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:05:47 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 60s. Last read position: chr1:164,468,682 INFO 2016-11-10 20:05:47 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:06:32 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 45s. Last read position: chr1:189,102,252 INFO 2016-11-10 20:06:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:07:03 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 30s. Last read position: chr1:213,979,760 INFO 2016-11-10 20:07:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:07:50 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 47s. Last read position: chr1:231,814,268 INFO 2016-11-10 20:07:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:08:40 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 49s. Last read position: chr2:3,652,468 INFO 2016-11-10 20:08:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:09:39 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 59s. Last read position: chr2:39,505,122 INFO 2016-11-10 20:09:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:10:30 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 51s. Last read position: chr2:73,561,393 INFO 2016-11-10 20:10:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:11:47 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 76s. Last read position: chr2:120,526,571 INFO 2016-11-10 20:11:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:12:27 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 39s. Last read position: chr2:160,316,783 INFO 2016-11-10 20:12:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:13:56 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 89s. Last read position: chr2:195,549,735 INFO 2016-11-10 20:13:56 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:14:48 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 51s. Last read position: chr2:230,358,034 INFO 2016-11-10 20:14:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:15:26 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 38s. Last read position: chr3:16,305,780 INFO 2016-11-10 20:15:26 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:17:11 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 104s. Last read position: chr3:49,251,279 INFO 2016-11-10 20:17:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:17:52 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:15:42s. Time for last 1,000,000: 41s. Last read position: chr3:84,621,225 INFO 2016-11-10 20:17:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:19:00 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 68s. Last read position: chr3:128,121,129 INFO 2016-11-10 20:19:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:19:39 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 38s. Last read position: chr3:165,373,238 INFO 2016-11-10 20:19:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:23:50 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:21:39s. Time for last 1,000,000: 250s. Last read position: chr3:195,333,247 INFO 2016-11-10 20:23:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:25:23 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:23:13s. Time for last 1,000,000: 93s. Last read position: chr4:37,752,582 INFO 2016-11-10 20:25:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:27:04 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:24:53s. Time for last 1,000,000: 100s. Last read position: chr4:81,286,306 INFO 2016-11-10 20:27:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:28:00 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:25:49s. Time for last 1,000,000: 56s. Last read position: chr4:119,339,736 INFO 2016-11-10 20:28:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:29:23 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:27:12s. Time for last 1,000,000: 82s. Last read position: chr4:158,818,783 INFO 2016-11-10 20:29:23 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:32:09 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:29:59s. Time for last 1,000,000: 166s. Last read position: chr5:6,447,551 INFO 2016-11-10 20:32:09 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-10 20:33:18 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:31:08s. Time for last 1,000,000: 69s. Last read position: chr5:33,219,021 INFO 2016-11-10 20:33:18 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:36:56 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:34:46s. Time for last 1,000,000: 218s. Last read position: chr5:60,694,078 INFO 2016-11-10 20:36:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:52:16 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:50:06s. Time for last 1,000,000: 919s. Last read position: chr5:86,336,676 INFO 2016-11-10 20:52:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:57:08 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:54:58s. Time for last 1,000,000: 292s. Last read position: chr5:112,930,184 INFO 2016-11-10 20:57:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:00:16 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:58:04s. Time for last 1,000,000: 185s. Last read position: chr5:136,852,889 INFO 2016-11-10 21:00:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:02:00 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:59:49s. Time for last 1,000,000: 105s. Last read position: chr5:160,271,193 INFO 2016-11-10 21:02:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:07:14 MarkDuplicates Read 34,000,000 records. Elapsed time: 01:05:04s. Time for last 1,000,000: 314s. Last read position: chr6:4,126,386 INFO 2016-11-10 21:07:14 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 21:16:18 MarkDuplicates Read 35,000,000 records. Elapsed time: 01:14:08s. Time for last 1,000,000: 543s. Last read position: chr6:28,666,579 INFO 2016-11-10 21:16:18 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:19:52 MarkDuplicates Read 36,000,000 records. Elapsed time: 01:17:42s. Time for last 1,000,000: 214s. Last read position: chr6:49,527,281 INFO 2016-11-10 21:19:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:21:32 MarkDuplicates Read 37,000,000 records. Elapsed time: 01:19:21s. Time for last 1,000,000: 99s. Last read position: chr6:81,728,195 INFO 2016-11-10 21:21:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:29:40 MarkDuplicates Read 38,000,000 records. Elapsed time: 01:27:29s. Time for last 1,000,000: 488s. Last read position: chr6:107,535,760 INFO 2016-11-10 21:29:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:35:22 MarkDuplicates Read 39,000,000 records. Elapsed time: 01:33:11s. Time for last 1,000,000: 342s. Last read position: chr6:132,364,408 INFO 2016-11-10 21:35:22 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 21:36:04 MarkDuplicates Read 40,000,000 records. Elapsed time: 01:33:54s. Time for last 1,000,000: 42s. Last read position: chr6:156,918,595 INFO 2016-11-10 21:36:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:37:31 MarkDuplicates Read 41,000,000 records. Elapsed time: 01:35:20s. Time for last 1,000,000: 86s. Last read position: chr7:18,636,743 INFO 2016-11-10 21:37:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:40:32 MarkDuplicates Read 42,000,000 records. Elapsed time: 01:38:22s. Time for last 1,000,000: 181s. Last read position: chr7:53,850,313 INFO 2016-11-10 21:40:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 21:44:59 MarkDuplicates Read 43,000,000 records. Elapsed time: 01:42:49s. Time for last 1,000,000: 266s. Last read position: chr7:96,503,433 INFO 2016-11-10 21:44:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 21:49:54 MarkDuplicates Read 44,000,000 records. Elapsed time: 01:47:44s. Time for last 1,000,000: 295s. Last read position: chr7:120,651,846 INFO 2016-11-10 21:49:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:02:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 02:00:45s. Time for last 1,000,000: 781s. Last read position: chr7:146,401,497 INFO 2016-11-10 22:02:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:09:23 MarkDuplicates Read 46,000,000 records. Elapsed time: 02:07:13s. Time for last 1,000,000: 387s. Last read position: chr8:17,030,519 INFO 2016-11-10 22:09:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:15:04 MarkDuplicates Read 47,000,000 records. Elapsed time: 02:12:54s. Time for last 1,000,000: 341s. Last read position: chr8:42,750,671 INFO 2016-11-10 22:15:04 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:15:36 MarkDuplicates Read 48,000,000 records. Elapsed time: 02:13:25s. Time for last 1,000,000: 31s. Last read position: chr8:85,385,487 INFO 2016-11-10 22:15:36 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:16:38 MarkDuplicates Read 49,000,000 records. Elapsed time: 02:14:28s. Time for last 1,000,000: 62s. Last read position: chr8:124,358,985 INFO 2016-11-10 22:16:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:32:50 MarkDuplicates Read 50,000,000 records. Elapsed time: 02:30:40s. Time for last 1,000,000: 972s. Last read position: chr9:18,183,883 INFO 2016-11-10 22:32:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:33:34 MarkDuplicates Read 51,000,000 records. Elapsed time: 02:31:24s. Time for last 1,000,000: 43s. Last read position: chr9:84,163,983 INFO 2016-11-10 22:33:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:34:08 MarkDuplicates Read 52,000,000 records. Elapsed time: 02:31:58s. Time for last 1,000,000: 34s. Last read position: chr9:119,875,535 INFO 2016-11-10 22:34:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:40:15 MarkDuplicates Read 53,000,000 records. Elapsed time: 02:38:05s. Time for last 1,000,000: 366s. Last read position: chr10:5,661,683 INFO 2016-11-10 22:40:15 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 22:42:10 MarkDuplicates Read 54,000,000 records. Elapsed time: 02:40:00s. Time for last 1,000,000: 114s. Last read position: chr10:29,748,948 INFO 2016-11-10 22:42:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:42:46 MarkDuplicates Read 55,000,000 records. Elapsed time: 02:40:36s. Time for last 1,000,000: 35s. Last read position: chr10:61,280,221 INFO 2016-11-10 22:42:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:47:38 MarkDuplicates Read 56,000,000 records. Elapsed time: 02:45:27s. Time for last 1,000,000: 291s. Last read position: chr10:85,305,552 INFO 2016-11-10 22:47:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:48:06 MarkDuplicates Read 57,000,000 records. Elapsed time: 02:45:56s. Time for last 1,000,000: 28s. Last read position: chr10:108,129,202 INFO 2016-11-10 22:48:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:48:15 MarkDuplicates Read 58,000,000 records. Elapsed time: 02:46:05s. Time for last 1,000,000: 8s. Last read position: chr10:132,730,123 INFO 2016-11-10 22:48:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:49:07 MarkDuplicates Read 59,000,000 records. Elapsed time: 02:46:57s. Time for last 1,000,000: 51s. Last read position: chr11:35,359,267 INFO 2016-11-10 22:49:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:50:07 MarkDuplicates Read 60,000,000 records. Elapsed time: 02:47:56s. Time for last 1,000,000: 59s. Last read position: chr11:75,696,431 INFO 2016-11-10 22:50:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:50:49 MarkDuplicates Read 61,000,000 records. Elapsed time: 02:48:38s. Time for last 1,000,000: 42s. Last read position: chr11:114,414,621 INFO 2016-11-10 22:50:49 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 22:51:21 MarkDuplicates Read 62,000,000 records. Elapsed time: 02:49:11s. Time for last 1,000,000: 32s. Last read position: chr12:8,900,276 INFO 2016-11-10 22:51:21 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 22:53:17 MarkDuplicates Read 63,000,000 records. Elapsed time: 02:51:07s. Time for last 1,000,000: 116s. Last read position: chr12:38,863,889 INFO 2016-11-10 22:53:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 22:53:35 MarkDuplicates Read 64,000,000 records. Elapsed time: 02:51:24s. Time for last 1,000,000: 17s. Last read position: chr12:60,598,824 INFO 2016-11-10 22:53:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:54:03 MarkDuplicates Read 65,000,000 records. Elapsed time: 02:51:53s. Time for last 1,000,000: 28s. Last read position: chr12:88,520,538 INFO 2016-11-10 22:54:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 22:54:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 02:52:20s. Time for last 1,000,000: 26s. Last read position: chr12:112,268,437 INFO 2016-11-10 22:54:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 22:56:10 MarkDuplicates Read 67,000,000 records. Elapsed time: 02:54:00s. Time for last 1,000,000: 99s. Last read position: chr13:23,999,632 INFO 2016-11-10 22:56:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:00:12 MarkDuplicates Read 68,000,000 records. Elapsed time: 02:58:02s. Time for last 1,000,000: 242s. Last read position: chr13:51,165,870 INFO 2016-11-10 23:00:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:01:12 MarkDuplicates Read 69,000,000 records. Elapsed time: 02:59:02s. Time for last 1,000,000: 59s. Last read position: chr13:88,986,369 INFO 2016-11-10 23:01:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:05:43 MarkDuplicates Read 70,000,000 records. Elapsed time: 03:03:32s. Time for last 1,000,000: 270s. Last read position: chr14:23,149,367 INFO 2016-11-10 23:05:43 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 23:06:20 MarkDuplicates Read 71,000,000 records. Elapsed time: 03:04:09s. Time for last 1,000,000: 36s. Last read position: chr14:58,140,905 INFO 2016-11-10 23:06:20 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:06:49 MarkDuplicates Read 72,000,000 records. Elapsed time: 03:04:38s. Time for last 1,000,000: 29s. Last read position: chr14:91,912,553 INFO 2016-11-10 23:06:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:07:20 MarkDuplicates Read 73,000,000 records. Elapsed time: 03:05:09s. Time for last 1,000,000: 31s. Last read position: chr15:38,895,095 INFO 2016-11-10 23:07:20 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:09:15 MarkDuplicates Read 74,000,000 records. Elapsed time: 03:07:03s. Time for last 1,000,000: 113s. Last read position: chr15:68,188,367 INFO 2016-11-10 23:09:15 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 23:11:40 MarkDuplicates Read 75,000,000 records. Elapsed time: 03:09:30s. Time for last 1,000,000: 146s. Last read position: chr15:87,921,272 INFO 2016-11-10 23:11:40 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:11:51 MarkDuplicates Read 76,000,000 records. Elapsed time: 03:09:40s. Time for last 1,000,000: 10s. Last read position: chr16:11,143,813 INFO 2016-11-10 23:11:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:14:26 MarkDuplicates Read 77,000,000 records. Elapsed time: 03:12:16s. Time for last 1,000,000: 155s. Last read position: chr16:51,391,437 INFO 2016-11-10 23:14:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:17:15 MarkDuplicates Read 78,000,000 records. Elapsed time: 03:15:05s. Time for last 1,000,000: 168s. Last read position: chr16:84,928,458 INFO 2016-11-10 23:17:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:19:43 MarkDuplicates Read 79,000,000 records. Elapsed time: 03:17:33s. Time for last 1,000,000: 148s. Last read position: chr17:18,368,935 INFO 2016-11-10 23:19:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:21:33 MarkDuplicates Read 80,000,000 records. Elapsed time: 03:19:23s. Time for last 1,000,000: 109s. Last read position: chr17:44,246,522 INFO 2016-11-10 23:21:33 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:23:57 MarkDuplicates Read 81,000,000 records. Elapsed time: 03:21:46s. Time for last 1,000,000: 143s. Last read position: chr17:66,172,158 INFO 2016-11-10 23:23:57 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 23:27:02 MarkDuplicates Read 82,000,000 records. Elapsed time: 03:24:51s. Time for last 1,000,000: 185s. Last read position: chr18:5,619,614 INFO 2016-11-10 23:27:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:28:28 MarkDuplicates Read 83,000,000 records. Elapsed time: 03:26:18s. Time for last 1,000,000: 86s. Last read position: chr18:46,152,631 INFO 2016-11-10 23:28:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:33:33 MarkDuplicates Read 84,000,000 records. Elapsed time: 03:31:23s. Time for last 1,000,000: 304s. Last read position: chr19:1,328,731 INFO 2016-11-10 23:33:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:34:52 MarkDuplicates Read 85,000,000 records. Elapsed time: 03:32:42s. Time for last 1,000,000: 79s. Last read position: chr19:28,148,444 INFO 2016-11-10 23:34:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:35:15 MarkDuplicates Read 86,000,000 records. Elapsed time: 03:33:05s. Time for last 1,000,000: 23s. Last read position: chr19:40,341,579 INFO 2016-11-10 23:35:15 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 23:35:38 MarkDuplicates Read 87,000,000 records. Elapsed time: 03:33:28s. Time for last 1,000,000: 22s. Last read position: chr20:3,222,035 INFO 2016-11-10 23:35:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:37:10 MarkDuplicates Read 88,000,000 records. Elapsed time: 03:34:59s. Time for last 1,000,000: 91s. Last read position: chr20:37,218,903 INFO 2016-11-10 23:37:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:39:57 MarkDuplicates Read 89,000,000 records. Elapsed time: 03:37:47s. Time for last 1,000,000: 167s. Last read position: chr20:62,871,367 INFO 2016-11-10 23:39:57 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 23:40:39 MarkDuplicates Read 90,000,000 records. Elapsed time: 03:38:29s. Time for last 1,000,000: 42s. Last read position: chr21:39,474,524 INFO 2016-11-10 23:40:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:41:25 MarkDuplicates Read 91,000,000 records. Elapsed time: 03:39:15s. Time for last 1,000,000: 45s. Last read position: chr22:31,346,944 INFO 2016-11-10 23:41:25 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 23:42:03 MarkDuplicates Read 92,000,000 records. Elapsed time: 03:39:52s. Time for last 1,000,000: 37s. Last read position: chrX:6,235,951 INFO 2016-11-10 23:42:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:43:12 MarkDuplicates Read 93,000,000 records. Elapsed time: 03:41:02s. Time for last 1,000,000: 69s. Last read position: chrX:38,820,975 INFO 2016-11-10 23:43:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 23:43:29 MarkDuplicates Read 94,000,000 records. Elapsed time: 03:41:19s. Time for last 1,000,000: 16s. Last read position: chrX:69,473,954 INFO 2016-11-10 23:43:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:43:47 MarkDuplicates Read 95,000,000 records. Elapsed time: 03:41:36s. Time for last 1,000,000: 17s. Last read position: chrX:92,683,143 INFO 2016-11-10 23:43:47 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 23:44:02 MarkDuplicates Read 96,000,000 records. Elapsed time: 03:41:52s. Time for last 1,000,000: 15s. Last read position: chrX:118,447,518 INFO 2016-11-10 23:44:02 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 23:44:20 MarkDuplicates Read 97,000,000 records. Elapsed time: 03:42:10s. Time for last 1,000,000: 18s. Last read position: chrX:142,819,613 INFO 2016-11-10 23:44:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:44:37 MarkDuplicates Read 98,000,000 records. Elapsed time: 03:42:27s. Time for last 1,000,000: 16s. Last read position: chrM:3,995 INFO 2016-11-10 23:44:37 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-10 23:44:57 MarkDuplicates Read 99,000,000 records. Elapsed time: 03:42:46s. Time for last 1,000,000: 19s. Last read position: chrM:11,775 INFO 2016-11-10 23:44:57 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-10 23:46:10 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-10 23:46:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 5530751112; totalMemory: 5612503040; maxMemory: 11453595648 INFO 2016-11-10 23:46:31 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 23:46:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 23:52:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 23:54:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 23:54:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 5633293432; totalMemory: 8575254528; maxMemory: 11453595648 INFO 2016-11-10 23:54:20 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-10 23:54:20 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-11 01:38:20 MarkDuplicates Written 10,000,000 records. Elapsed time: 01:43:34s. Time for last 10,000,000: 6,214s. Last read position: chr2:3,652,468 INFO 2016-11-11 02:49:58 MarkDuplicates Written 20,000,000 records. Elapsed time: 02:55:13s. Time for last 10,000,000: 4,298s. Last read position: chr3:128,121,129 INFO 2016-11-11 04:21:22 MarkDuplicates Written 30,000,000 records. Elapsed time: 04:26:37s. Time for last 10,000,000: 5,484s. Last read position: chr5:86,336,676 INFO 2016-11-11 05:02:03 MarkDuplicates Written 40,000,000 records. Elapsed time: 05:07:18s. Time for last 10,000,000: 2,440s. Last read position: chr6:156,918,595 INFO 2016-11-11 05:36:07 MarkDuplicates Written 50,000,000 records. Elapsed time: 05:41:21s. Time for last 10,000,000: 2,043s. Last read position: chr9:18,183,883 INFO 2016-11-11 05:51:42 MarkDuplicates Written 60,000,000 records. Elapsed time: 05:56:57s. Time for last 10,000,000: 935s. Last read position: chr11:75,696,431 INFO 2016-11-11 06:17:18 MarkDuplicates Written 70,000,000 records. Elapsed time: 06:22:33s. Time for last 10,000,000: 1,536s. Last read position: chr14:23,149,367 INFO 2016-11-11 06:40:14 MarkDuplicates Written 80,000,000 records. Elapsed time: 06:45:28s. Time for last 10,000,000: 1,375s. Last read position: chr17:44,246,522 INFO 2016-11-11 06:57:12 MarkDuplicates Written 90,000,000 records. Elapsed time: 07:02:27s. Time for last 10,000,000: 1,018s. Last read position: chr21:39,474,524 INFO 2016-11-11 07:03:09 MarkDuplicates Before output close freeMemory: 8495780416; totalMemory: 8579973120; maxMemory: 11453595648 INFO 2016-11-11 07:03:42 MarkDuplicates After output close freeMemory: 8497874672; totalMemory: 8582070272; maxMemory: 11453595648 [Fri Nov 11 07:03:43 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 662.60 minutes. Runtime.totalMemory()=8582070272 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
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 147
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/rep1/SRR1370897_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370897_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/rep1/SRR1370897_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/align/rep1/SRR1370897_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370897_1/out/qc/rep1/SRR1370897_1.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 20931 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.23 sec [bwa_aln_core] refine gapped alignments... 1.23 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 1.04 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.09 sec [bwa_aln_core] refine gapped alignments... 0.86 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.96 sec [bwa_aln_core] refine gapped alignments... 0.78 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 786432 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... 2.25 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.18 sec [bwa_aln_core] refine gapped alignments... 0.83 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.18 sec [bwa_aln_core] refine gapped alignments... 0.78 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.14 sec [bwa_aln_core] refine gapped alignments... 1.50 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.86 sec [bwa_aln_core] refine gapped alignments... 1.25 sec [bwa_aln_core] print alignments... 0.94 sec [bwa_aln_core] 2097152 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... 0.80 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.34 sec [bwa_aln_core] refine gapped alignments... 2.38 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.44 sec [bwa_aln_core] refine gapped alignments... 2.33 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.68 sec [bwa_aln_core] refine gapped alignments... 2.13 sec [bwa_aln_core] print alignments... 0.87 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.93 sec [bwa_aln_core] refine gapped alignments... 2.32 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.10 sec [bwa_aln_core] refine gapped alignments... 2.31 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.14 sec [bwa_aln_core] refine gapped alignments... 2.37 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.90 sec [bwa_aln_core] refine gapped alignments... 2.53 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.69 sec [bwa_aln_core] refine gapped alignments... 2.32 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.87 sec [bwa_aln_core] refine gapped alignments... 2.33 sec [bwa_aln_core] print alignments... 0.83 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.27 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.64 sec [bwa_aln_core] refine gapped alignments... 2.51 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.69 sec [bwa_aln_core] refine gapped alignments... 2.59 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.35 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.11 sec [bwa_aln_core] refine gapped alignments... 2.48 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.70 sec [bwa_aln_core] refine gapped alignments... 2.61 sec [bwa_aln_core] print alignments... 0.84 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.63 sec [bwa_aln_core] refine gapped alignments... 2.57 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.70 sec [bwa_aln_core] refine gapped alignments... 2.07 sec [bwa_aln_core] print alignments... 1.06 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.55 sec [bwa_aln_core] refine gapped alignments... 2.60 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.44 sec [bwa_aln_core] refine gapped alignments... 1.23 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.66 sec [bwa_aln_core] refine gapped alignments... 0.98 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.61 sec [bwa_aln_core] refine gapped alignments... 1.81 sec [bwa_aln_core] print alignments... 0.86 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.24 sec [bwa_aln_core] refine gapped alignments... 2.09 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.34 sec [bwa_aln_core] refine gapped alignments... 2.15 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.79 sec [bwa_aln_core] refine gapped alignments... 2.17 sec [bwa_aln_core] print alignments... 0.94 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.94 sec [bwa_aln_core] refine gapped alignments... 1.94 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.94 sec [bwa_aln_core] refine gapped alignments... 0.91 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.44 sec [bwa_aln_core] refine gapped alignments... 1.99 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.80 sec [bwa_aln_core] refine gapped alignments... 3.46 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.28 sec [bwa_aln_core] refine gapped alignments... 2.04 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.85 sec [bwa_aln_core] refine gapped alignments... 2.80 sec [bwa_aln_core] print alignments... 1.15 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.00 sec [bwa_aln_core] refine gapped alignments... 2.65 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 10485760 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... 0.94 sec [bwa_aln_core] print alignments... 1.01 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.31 sec [bwa_aln_core] refine gapped alignments... 1.05 sec [bwa_aln_core] print alignments... 0.95 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.80 sec [bwa_aln_core] refine gapped alignments... 0.78 sec [bwa_aln_core] print alignments... 1.05 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.76 sec [bwa_aln_core] refine gapped alignments... 1.36 sec [bwa_aln_core] print alignments... 0.98 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.31 sec [bwa_aln_core] refine gapped alignments... 1.44 sec [bwa_aln_core] print alignments... 1.10 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.51 sec [bwa_aln_core] refine gapped alignments... 0.76 sec [bwa_aln_core] print alignments... 0.86 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.62 sec [bwa_aln_core] refine gapped alignments... 1.80 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.78 sec [bwa_aln_core] refine gapped alignments... 0.77 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 92.53 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.78 sec [bwa_aln_core] refine gapped alignments... 1.39 sec [bwa_aln_core] print alignments... 0.92 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.17 sec [bwa_aln_core] refine gapped alignments... 1.19 sec [bwa_aln_core] print alignments... 0.99 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.04 sec [bwa_aln_core] refine gapped alignments... 1.07 sec [bwa_aln_core] print alignments... 0.96 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.12 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.19 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 1.09 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.46 sec [bwa_aln_core] refine gapped alignments... 1.97 sec [bwa_aln_core] print alignments... 1.00 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.44 sec [bwa_aln_core] refine gapped alignments... 1.19 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 82.92 sec [bwa_aln_core] refine gapped alignments... 2.32 sec [bwa_aln_core] print alignments... 0.93 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.96 sec [bwa_aln_core] refine gapped alignments... 2.37 sec [bwa_aln_core] print alignments... 1.11 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 430.30 sec [bwa_aln_core] refine gapped alignments... 2.05 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 214.30 sec [bwa_aln_core] refine gapped alignments... 3.35 sec [bwa_aln_core] print alignments... 1.30 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.88 sec [bwa_aln_core] refine gapped alignments... 1.42 sec [bwa_aln_core] print alignments... 1.14 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 86.02 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 1.15 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.16 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 88.24 sec [bwa_aln_core] refine gapped alignments... 0.99 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.26 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 1.10 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.17 sec [bwa_aln_core] refine gapped alignments... 0.97 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.71 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 1.30 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.63 sec [bwa_aln_core] refine gapped alignments... 2.32 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.11 sec [bwa_aln_core] refine gapped alignments... 0.77 sec [bwa_aln_core] print alignments... 1.40 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.93 sec [bwa_aln_core] refine gapped alignments... 0.70 sec [bwa_aln_core] print alignments... 1.30 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.09 sec [bwa_aln_core] refine gapped alignments... 0.88 sec [bwa_aln_core] print alignments... 1.47 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.37 sec [bwa_aln_core] refine gapped alignments... 0.74 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.48 sec [bwa_aln_core] refine gapped alignments... 0.87 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.37 sec [bwa_aln_core] refine gapped alignments... 0.76 sec [bwa_aln_core] print alignments... 1.27 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 169.59 sec [bwa_aln_core] refine gapped alignments... 1.72 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.74 sec [bwa_aln_core] refine gapped alignments... 0.96 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.72 sec [bwa_aln_core] refine gapped alignments... 1.06 sec [bwa_aln_core] print alignments... 0.87 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.75 sec [bwa_aln_core] refine gapped alignments... 0.71 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.20 sec [bwa_aln_core] refine gapped alignments... 1.05 sec [bwa_aln_core] print alignments... 0.95 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.82 sec [bwa_aln_core] refine gapped alignments... 0.72 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.60 sec [bwa_aln_core] refine gapped alignments... 0.74 sec [bwa_aln_core] print alignments... 0.89 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.63 sec [bwa_aln_core] refine gapped alignments... 0.99 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.28 sec [bwa_aln_core] refine gapped alignments... 1.33 sec [bwa_aln_core] print alignments... 0.86 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.40 sec [bwa_aln_core] refine gapped alignments... 0.68 sec [bwa_aln_core] print alignments... 0.98 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.73 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.81 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.77 sec [bwa_aln_core] refine gapped alignments... 0.69 sec [bwa_aln_core] print alignments... 0.94 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.23 sec [bwa_aln_core] refine gapped alignments... 0.70 sec [bwa_aln_core] print alignments... 0.86 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.91 sec [bwa_aln_core] refine gapped alignments... 0.66 sec [bwa_aln_core] print alignments... 0.88 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.38 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.91 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.20 sec [bwa_aln_core] refine gapped alignments... 0.66 sec [bwa_aln_core] print alignments... 0.97 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.89 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.96 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.21 sec [bwa_aln_core] refine gapped alignments... 0.75 sec [bwa_aln_core] print alignments... 0.90 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.50 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 0.85 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.01 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 24555168 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/HughesZnfData/SRR1370897_1/out/align/rep1/SRR1370897_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370897_1.fastq.gz [main] Real time: 13244.013 sec; CPU: 3238.512 sec |
| Type | Name | Value |
|---|---|---|
| int{} | filesize | {rep1=3722572281, ctl1=11033042636} |
| int{} | nth_rep | {rep1=1, ctl1=4} |