Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.align_bwa.bwa_aln_ctl1.line_111.id_10 | Name | bwa_aln ctl1 | Thread | thread_42 | PID | 35892 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-28 23:03:16 | End | 2017-01-29 00:01:39 | Elapsed | 00:58:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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--------------------
56883 (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] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17560427 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/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 3477.270 sec; CPU: 3471.932 sec
|
Num | 2 | ID | task.align_bwa.bwa_aln_rep1.line_111.id_11 | Name | bwa_aln rep1 | Thread | thread_41 | PID | 35893 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 23:03:17 | End | 2017-01-28 23:57:31 | Elapsed | 00:54:14 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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--------------------
56882 (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] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.65 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.43 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.32 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.94 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.13 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.71 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.06 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.65 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.97 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.84 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.02 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.89 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.16 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.05 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.38 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.49 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.33 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.70 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.21 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.22 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.90 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.01 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.11 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.67 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.63 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.75 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.10 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.94 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.46 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.26 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.91 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.39 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.38 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.83 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.84 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.77 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.72 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.66 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.87 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.54 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.47 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.72 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.20 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.39 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.73 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.13 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.59 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.85 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.02 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.03 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.37 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.45 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.86 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.49 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.72 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.46 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.68 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.31 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24329011 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz
[main] Real time: 3228.925 sec; CPU: 8384.736 sec
|
Num | 3 | ID | task.align_bwa.bwa_sam_rep1.line_143.id_12 | Name | bwa_sam rep1 | Thread | thread_41 | PID | 35934 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-28 23:57:32 | End | 2017-01-29 00:33:27 | Elapsed | 00:35:54 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.sai
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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/Liu2013Data/EP300/out/align/rep1/SRR1016004.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam
# SYS command. line 152
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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--------------------
59407 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.83 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.13 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.95 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.26 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.35 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.05 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.05 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.61 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.90 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.11 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.67 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.05 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.02 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.59 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.82 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.08 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.46 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.80 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.10 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.36 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.62 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.85 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.59 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.01 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.72 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.64 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.70 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.23 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.32 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.40 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.43 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.54 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.16 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.95 sec
[bwa_aln_core] refine gapped alignments... 2.43 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.63 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.27 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.06 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.22 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.16 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.34 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.20 sec
[bwa_aln_core] refine gapped alignments... 2.45 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.39 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.66 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.63 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.51 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.27 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.82 sec
[bwa_aln_core] refine gapped alignments... 2.43 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.16 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.40 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.57 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.57 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.80 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.32 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.00 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.32 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.60 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.48 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.61 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.66 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.93 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.94 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.58 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.90 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.39 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.32 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.34 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.34 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.42 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.72 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.46 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.59 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 2.46 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.41 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.57 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.14 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.01 sec
[bwa_aln_core] refine gapped alignments... 2.77 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.38 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.38 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 24329011 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/Liu2013Data/EP300/out/align/rep1/SRR1016004.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1016004.fastq.gz
[main] Real time: 1874.441 sec; CPU: 1805.772 sec
|
Num | 4 | ID | task.align_bwa.bwa_sam_ctl1.line_143.id_13 | Name | bwa_sam ctl1 | Thread | thread_42 | PID | 35944 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-29 00:01:40 | End | 2017-01-29 00:36:41 | Elapsed | 00:35:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.sai
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.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/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam
# SYS command. line 152
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.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--------------------
59830 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.94 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.79 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.05 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.30 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.45 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.31 sec
[bwa_aln_core] refine gapped alignments... 2.48 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.33 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.44 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.32 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.44 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.07 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.62 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.69 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.11 sec
[bwa_aln_core] refine gapped alignments... 2.80 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.32 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.56 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.15 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.70 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.76 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.00 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.24 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.54 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 2.48 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.65 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.61 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.04 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.25 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.44 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.15 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.47 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.97 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.29 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.27 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.99 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.46 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.14 sec
[bwa_aln_core] refine gapped alignments... 2.98 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.12 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.31 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.79 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.72 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.78 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.04 sec
[bwa_aln_core] refine gapped alignments... 2.13 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.74 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.43 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.67 sec
[bwa_aln_core] refine gapped alignments... 2.11 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.26 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.23 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.90 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.02 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.27 sec
[bwa_aln_core] refine gapped alignments... 2.19 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.47 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.69 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.88 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.92 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.06 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.10 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.64 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.55 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.87 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 17560427 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/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 1587.718 sec; CPU: 1479.592 sec
|
Num | 5 | ID | task.postalign_bam.dedup_bam_1_rep1.line_95.id_14 | Name | dedup_bam_1 rep1 | Thread | thread_41 | PID | 35991 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-29 00:33:28 | End | 2017-01-29 00:36:03 | Elapsed | 00:02:34 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.bam | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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--------------------
56566 (process ID) old priority 0, new priority 10
|
Num | 6 | ID | task.postalign_bam.markdup_bam_picard_rep1.line_348.id_15 | Name | markdup_bam_picard rep1 | Thread | thread_41 | PID | 35996 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-29 00:36:05 | End | 2017-01-29 00:40:46 | Elapsed | 00:04:41 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.filt.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
7947 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:36:21 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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 00:36:21 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 00:36:21 MarkDuplicates Start of doWork freeMemory: 254879616; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-29 00:36:21 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-29 00:36:21 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
WARNING 2017-01-29 00:36:24 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1016004.16702886'. 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 00:36:31 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:112,646,277
INFO 2017-01-29 00:36:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:36:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 6s. Last read position: chr2:16,248,915
INFO 2017-01-29 00:36:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:36:41 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr2:181,003,693
INFO 2017-01-29 00:36:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:36:46 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 4s. Last read position: chr3:99,561,461
INFO 2017-01-29 00:36:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:36:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 7s. Last read position: chr4:54,478,375
INFO 2017-01-29 00:36:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:36:56 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr5:93,050,878
INFO 2017-01-29 00:36:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:03 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: chr6:62,975,032
INFO 2017-01-29 00:37:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:05 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr7:28,685,091
INFO 2017-01-29 00:37:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:11 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 6s. Last read position: chr8:56,211,788
INFO 2017-01-29 00:37:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:15 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr9:134,140,869
INFO 2017-01-29 00:37:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:19 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 4s. Last read position: chr11:7,219,549
INFO 2017-01-29 00:37:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:23 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 4s. Last read position: chr12:27,005,605
INFO 2017-01-29 00:37:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:26 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr13:73,506,591
INFO 2017-01-29 00:37:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:37 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 11s. Last read position: chr15:65,768,667
INFO 2017-01-29 00:37:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:40 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr17:3,172,659
INFO 2017-01-29 00:37:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:44 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 4s. Last read position: chr19:1,173,533
INFO 2017-01-29 00:37:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:47 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr21:27,801,878
INFO 2017-01-29 00:37:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:37:49 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chrX:99,496,732
INFO 2017-01-29 00:37:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:38:00 MarkDuplicates Read 18358697 records. 0 pairs never matched.
INFO 2017-01-29 00:38:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 4404567448; totalMemory: 6011486208; maxMemory: 11453595648
INFO 2017-01-29 00:38:02 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-29 00:38:02 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-29 00:38:02 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-29 00:38:03 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-29 00:38:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 5935459584; totalMemory: 8876720128; maxMemory: 11453595648
INFO 2017-01-29 00:38:25 MarkDuplicates Marking 171413 records as duplicates.
INFO 2017-01-29 00:38:25 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-29 00:39:38 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:13s. Time for last 10,000,000: 73s. Last read position: chr9:134,140,869
INFO 2017-01-29 00:40:44 MarkDuplicates Before output close freeMemory: 8817093384; totalMemory: 8898740224; maxMemory: 11453595648
INFO 2017-01-29 00:40:45 MarkDuplicates After output close freeMemory: 8679728768; totalMemory: 8761376768; maxMemory: 11453595648
[Sun Jan 29 00:40:45 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.39 minutes.
Runtime.totalMemory()=8761376768
|
Num | 7 | ID | task.postalign_bam.dedup_bam_1_ctl1.line_95.id_16 | Name | dedup_bam_1 ctl1 | Thread | thread_42 | PID | 35997 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:36:42 | End | 2017-01-29 00:40:07 | Elapsed | 00:03:24 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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--------------------
10673 (process ID) old priority 0, new priority 10
|
Num | 8 | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_17 | Name | markdup_bam_picard ctl1 | Thread | thread_42 | PID | 36001 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2017-01-29 00:40:08 | End | 2017-01-29 00:43:06 | Elapsed | 00:02:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.filt.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
8165 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:40:22 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.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 00:40:22 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 00:40:22 MarkDuplicates Start of doWork freeMemory: 254879592; totalMemory: 257425408; maxMemory: 11453595648
INFO 2017-01-29 00:40:22 MarkDuplicates Reading input file and constructing read end information.
INFO 2017-01-29 00:40:22 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
INFO 2017-01-29 00:40:32 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr2:7,720,599
INFO 2017-01-29 00:40:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:40:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 5s. Last read position: chr3:32,290,878
INFO 2017-01-29 00:40:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:40:42 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 4s. Last read position: chr5:31,410,244
INFO 2017-01-29 00:40:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:40:47 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 4s. Last read position: chr6:76,055,404
INFO 2017-01-29 00:40:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:40:51 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr7:134,138,515
INFO 2017-01-29 00:40:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:40:56 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 5s. Last read position: chr9:137,609,223
INFO 2017-01-29 00:40:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:00 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 3s. Last read position: chr11:121,062,334
INFO 2017-01-29 00:41:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:04 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 4s. Last read position: chr14:86,188,790
INFO 2017-01-29 00:41:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:09 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 5s. Last read position: chr17:58,813,264
INFO 2017-01-29 00:41:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:15 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 5s. Last read position: chr20:35,666,706
INFO 2017-01-29 00:41:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:17 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chrX:100,440,272
INFO 2017-01-29 00:41:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2017-01-29 00:41:20 MarkDuplicates Read 11369002 records. 0 pairs never matched.
INFO 2017-01-29 00:41:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 3443408512; totalMemory: 4590665728; maxMemory: 11453595648
INFO 2017-01-29 00:41:22 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk.
INFO 2017-01-29 00:41:24 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2017-01-29 00:41:24 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2017-01-29 00:41:24 MarkDuplicates Sorting list of duplicate records.
INFO 2017-01-29 00:41:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 1660781408; totalMemory: 4590665728; maxMemory: 11453595648
INFO 2017-01-29 00:41:26 MarkDuplicates Marking 167589 records as duplicates.
INFO 2017-01-29 00:41:26 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2017-01-29 00:42:55 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:28s. Time for last 10,000,000: 88s. Last read position: chr20:35,666,706
INFO 2017-01-29 00:43:05 MarkDuplicates Before output close freeMemory: 8027380208; totalMemory: 8107065344; maxMemory: 11453595648
INFO 2017-01-29 00:43:05 MarkDuplicates After output close freeMemory: 8128566632; totalMemory: 8208252928; maxMemory: 11453595648
[Sun Jan 29 00:43:06 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.73 minutes.
Runtime.totalMemory()=8208252928
|
Num | 9 | ID | task.postalign_bam.dedup_bam_2_rep1.line_144.id_18 | Name | dedup_bam_2 rep1 | Thread | thread_41 | PID | 36002 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-29 00:40:47 | End | 2017-01-29 00:45:27 | Elapsed | 00:04:39 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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/Liu2013Data/EP300/out/align/rep1/SRR1016004.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam
# SYS command. line 153
sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam
# SYS command. line 155
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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--------------------
26247 (process ID) old priority 0, new priority 10
|
Num | 10 | ID | task.postalign_bam.dedup_bam_2_ctl1.line_144.id_19 | Name | dedup_bam_2 ctl1 | Thread | thread_42 | PID | 36005 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:43:08 | End | 2017-01-29 00:46:12 | Elapsed | 00:03:03 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.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/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/ctl1/ENCFF001HNC.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
34282 (process ID) old priority 0, new priority 10
|
Num | 11 | ID | task.postalign_bam.bam_to_tag_rep1.line_505.id_20 | Name | bam_to_tag rep1 | Thread | thread_41 | PID | 36011 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:45:29 | End | 2017-01-29 00:46:52 | Elapsed | 00:01:23 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
42810 (process ID) old priority 0, new priority 10
Waiting for 19 seconds.
|
Num | 12 | ID | task.postalign_bam.bam_to_tag_ctl1.line_505.id_21 | Name | bam_to_tag ctl1 | Thread | thread_42 | PID | 36012 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:46:13 | End | 2017-01-29 00:47:36 | Elapsed | 00:01:22 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Dependencies | | |
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
45303 (process ID) old priority 0, new priority 10
Waiting for 36 seconds.
|
Num | 13 | ID | task.postalign_bed.subsample_tag_rep1.line_45.id_22 | Name | subsample_tag rep1 | Thread | thread_41 | PID | 36013 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:46:53 | End | 2017-01-29 00:48:05 | Elapsed | 00:01:12 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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--------------------
47062 (process ID) old priority 0, new priority 10
Waiting for 30 seconds.
|
Num | 14 | ID | task.postalign_bed.spr_rep1.line_255.id_23 | Name | spr rep1 | Thread | thread_41 | PID | 36014 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:46:55 | End | 2017-01-29 00:48:06 | Elapsed | 00:01:11 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.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=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
47063 (process ID) old priority 0, new priority 10
Waiting for 23 seconds.
|
Num | 15 | ID | task.postalign_bed.xcor_rep1.line_212.id_24 | Name | xcor rep1 | Thread | thread_41 | PID | 36018 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 3 | Mem | | | Start | 2017-01-29 00:48:08 | End | 2017-01-29 00:56:37 | Elapsed | 00:08:28 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.15M.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.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--------------------
51775 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.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: 3
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/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/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.15M.tagAlign.gz
opened /tmp/36018.1.q/Rtmpf5Z7Tj/SRR1016004.nodup.15M.tagAligncc215eaaaf2e
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1738318
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.179409894013095,0.179300958682944,0.177937701153907
Top 3 estimates for fragment length 100,125,220
Window half size 415
Phantom peak location 50
Phantom peak Correlation 0.1794658
Normalized Strand cross-correlation coefficient (NSC) 1.032089
Relative Strand cross-correlation Coefficient (RSC) 0.9900716
Phantom Peak Quality Tag 0
null device
1
--------------------Stderr--------------------
Loading required package: caTools
|
Num | 16 | ID | task.callpeak_macs2.macs2_rep1.line_71.id_25 | Name | macs2 rep1 | Thread | thread_Root | PID | 36035 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:56:39 | End | 2017-01-29 01:20:30 | Elapsed | 00:23:51 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/signal/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/signal/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ true == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1 -o "SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/signal/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1 -o "SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/signal/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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--------------------
27069 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:56:53:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 00:56:53: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:56:53: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:56:55: 1000000
INFO @ Sun, 29 Jan 2017 00:56:56: 2000000
INFO @ Sun, 29 Jan 2017 00:56:58: 3000000
INFO @ Sun, 29 Jan 2017 00:56:59: 4000000
INFO @ Sun, 29 Jan 2017 00:57:00: 5000000
INFO @ Sun, 29 Jan 2017 00:57:02: 6000000
INFO @ Sun, 29 Jan 2017 00:57:03: 7000000
INFO @ Sun, 29 Jan 2017 00:57:04: 8000000
INFO @ Sun, 29 Jan 2017 00:57:06: 9000000
INFO @ Sun, 29 Jan 2017 00:57:07: 10000000
INFO @ Sun, 29 Jan 2017 00:57:09: 11000000
INFO @ Sun, 29 Jan 2017 00:57:10: 12000000
INFO @ Sun, 29 Jan 2017 00:57:11: 13000000
INFO @ Sun, 29 Jan 2017 00:57:13: 14000000
INFO @ Sun, 29 Jan 2017 00:57:14: 15000000
INFO @ Sun, 29 Jan 2017 00:57:16: 16000000
INFO @ Sun, 29 Jan 2017 00:57:17: 17000000
INFO @ Sun, 29 Jan 2017 00:57:18: 18000000
INFO @ Sun, 29 Jan 2017 00:57:19: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:57:20: 1000000
INFO @ Sun, 29 Jan 2017 00:57:22: 2000000
INFO @ Sun, 29 Jan 2017 00:57:23: 3000000
INFO @ Sun, 29 Jan 2017 00:57:24: 4000000
INFO @ Sun, 29 Jan 2017 00:57:26: 5000000
INFO @ Sun, 29 Jan 2017 00:57:27: 6000000
INFO @ Sun, 29 Jan 2017 00:57:29: 7000000
INFO @ Sun, 29 Jan 2017 00:57:30: 8000000
INFO @ Sun, 29 Jan 2017 00:57:31: 9000000
INFO @ Sun, 29 Jan 2017 00:57:33: 10000000
INFO @ Sun, 29 Jan 2017 00:57:34: 11000000
INFO @ Sun, 29 Jan 2017 00:57:35: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 00:57:35: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 00:57:35: #1 total tags in treatment: 18187284
INFO @ Sun, 29 Jan 2017 00:57:35: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:57:35: #1 finished!
INFO @ Sun, 29 Jan 2017 00:57:35: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:57:35: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:57:35: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 00:57:35: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:57:35: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:57:35: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:58:32: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:58:32: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:58:32: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:58:32: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:58:32: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 01:00:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 01:00:50: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 01:00:50: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 01:00:51: Done!
INFO @ Sun, 29 Jan 2017 01:00:52:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/rep1/SRR1016004.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 01:00:52: #1 read tag files...
INFO @ Sun, 29 Jan 2017 01:00:52: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 01:00:54: 1000000
INFO @ Sun, 29 Jan 2017 01:00:55: 2000000
INFO @ Sun, 29 Jan 2017 01:00:57: 3000000
INFO @ Sun, 29 Jan 2017 01:00:58: 4000000
INFO @ Sun, 29 Jan 2017 01:00:59: 5000000
INFO @ Sun, 29 Jan 2017 01:01:01: 6000000
INFO @ Sun, 29 Jan 2017 01:01:02: 7000000
INFO @ Sun, 29 Jan 2017 01:01:04: 8000000
INFO @ Sun, 29 Jan 2017 01:01:05: 9000000
INFO @ Sun, 29 Jan 2017 01:01:06: 10000000
INFO @ Sun, 29 Jan 2017 01:01:08: 11000000
INFO @ Sun, 29 Jan 2017 01:01:09: 12000000
INFO @ Sun, 29 Jan 2017 01:01:11: 13000000
INFO @ Sun, 29 Jan 2017 01:01:12: 14000000
INFO @ Sun, 29 Jan 2017 01:01:13: 15000000
INFO @ Sun, 29 Jan 2017 01:01:15: 16000000
INFO @ Sun, 29 Jan 2017 01:01:16: 17000000
INFO @ Sun, 29 Jan 2017 01:01:18: 18000000
INFO @ Sun, 29 Jan 2017 01:01:18: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 01:01:20: 1000000
INFO @ Sun, 29 Jan 2017 01:01:21: 2000000
INFO @ Sun, 29 Jan 2017 01:01:22: 3000000
INFO @ Sun, 29 Jan 2017 01:01:24: 4000000
INFO @ Sun, 29 Jan 2017 01:01:25: 5000000
INFO @ Sun, 29 Jan 2017 01:01:27: 6000000
INFO @ Sun, 29 Jan 2017 01:01:28: 7000000
INFO @ Sun, 29 Jan 2017 01:01:29: 8000000
INFO @ Sun, 29 Jan 2017 01:01:31: 9000000
INFO @ Sun, 29 Jan 2017 01:01:32: 10000000
INFO @ Sun, 29 Jan 2017 01:01:33: 11000000
INFO @ Sun, 29 Jan 2017 01:01:34: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 01:01:34: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 01:01:34: #1 total tags in treatment: 18187284
INFO @ Sun, 29 Jan 2017 01:01:34: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 01:01:34: #1 finished!
INFO @ Sun, 29 Jan 2017 01:01:34: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 01:01:34: #2 Skipped...
INFO @ Sun, 29 Jan 2017 01:01:34: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 01:01:34: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 01:01:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 01:01:34: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 01:02:23: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 01:03:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 01:03:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 01:03:14: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 01:03:16: Done!
INFO @ Sun, 29 Jan 2017 01:03:26: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 01:04:01: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 01:04:34: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 01:05:05: Calculate scores comparing treatment and control by 'FE'...
INFO @ Sun, 29 Jan 2017 01:07:30: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 01:09:04: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'!
INFO @ Sun, 29 Jan 2017 01:12:18: Read and build treatment bedGraph...
INFO @ Sun, 29 Jan 2017 01:12:53: Read and build control bedGraph...
INFO @ Sun, 29 Jan 2017 01:13:26: Build scoreTrackII...
INFO @ Sun, 29 Jan 2017 01:13:45: Values in your input bedGraph files will be multiplied by 11.201413 ...
INFO @ Sun, 29 Jan 2017 01:16:09: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Sun, 29 Jan 2017 01:16:27: Write bedGraph of scores...
INFO @ Sun, 29 Jan 2017 01:17:34: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'!
|
Num | 17 | ID | task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26 | Name | macs2 rep1-pr1 | Thread | thread_Root | PID | 36036 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:56:40 | End | 2017-01-29 01:03:16 | Elapsed | 00:06:36 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.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--------------------
27067 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:56:53:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 00:56:53: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:56:53: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:56:55: 1000000
INFO @ Sun, 29 Jan 2017 00:56:57: 2000000
INFO @ Sun, 29 Jan 2017 00:56:58: 3000000
INFO @ Sun, 29 Jan 2017 00:57:00: 4000000
INFO @ Sun, 29 Jan 2017 00:57:01: 5000000
INFO @ Sun, 29 Jan 2017 00:57:03: 6000000
INFO @ Sun, 29 Jan 2017 00:57:05: 7000000
INFO @ Sun, 29 Jan 2017 00:57:06: 8000000
INFO @ Sun, 29 Jan 2017 00:57:08: 9000000
INFO @ Sun, 29 Jan 2017 00:57:09: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:57:10: 1000000
INFO @ Sun, 29 Jan 2017 00:57:11: 2000000
INFO @ Sun, 29 Jan 2017 00:57:13: 3000000
INFO @ Sun, 29 Jan 2017 00:57:14: 4000000
INFO @ Sun, 29 Jan 2017 00:57:16: 5000000
INFO @ Sun, 29 Jan 2017 00:57:17: 6000000
INFO @ Sun, 29 Jan 2017 00:57:19: 7000000
INFO @ Sun, 29 Jan 2017 00:57:20: 8000000
INFO @ Sun, 29 Jan 2017 00:57:22: 9000000
INFO @ Sun, 29 Jan 2017 00:57:23: 10000000
INFO @ Sun, 29 Jan 2017 00:57:24: 11000000
INFO @ Sun, 29 Jan 2017 00:57:25: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 00:57:25: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 00:57:25: #1 total tags in treatment: 9093642
INFO @ Sun, 29 Jan 2017 00:57:25: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:57:25: #1 finished!
INFO @ Sun, 29 Jan 2017 00:57:25: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:57:25: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:57:25: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 00:57:25: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:57:25: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:57:25: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:58:13: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:58:13: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:58:13: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:58:13: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:58:13: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:59:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 01:00:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 01:00:01: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 01:00:01: Done!
INFO @ Sun, 29 Jan 2017 01:00:04:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 01:00:04: #1 read tag files...
INFO @ Sun, 29 Jan 2017 01:00:04: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 01:00:06: 1000000
INFO @ Sun, 29 Jan 2017 01:00:07: 2000000
INFO @ Sun, 29 Jan 2017 01:00:09: 3000000
INFO @ Sun, 29 Jan 2017 01:00:11: 4000000
INFO @ Sun, 29 Jan 2017 01:00:12: 5000000
INFO @ Sun, 29 Jan 2017 01:00:14: 6000000
INFO @ Sun, 29 Jan 2017 01:00:16: 7000000
INFO @ Sun, 29 Jan 2017 01:00:17: 8000000
INFO @ Sun, 29 Jan 2017 01:00:19: 9000000
INFO @ Sun, 29 Jan 2017 01:00:19: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 01:00:21: 1000000
INFO @ Sun, 29 Jan 2017 01:00:22: 2000000
INFO @ Sun, 29 Jan 2017 01:00:23: 3000000
INFO @ Sun, 29 Jan 2017 01:00:25: 4000000
INFO @ Sun, 29 Jan 2017 01:00:26: 5000000
INFO @ Sun, 29 Jan 2017 01:00:28: 6000000
INFO @ Sun, 29 Jan 2017 01:00:29: 7000000
INFO @ Sun, 29 Jan 2017 01:00:30: 8000000
INFO @ Sun, 29 Jan 2017 01:00:32: 9000000
INFO @ Sun, 29 Jan 2017 01:00:33: 10000000
INFO @ Sun, 29 Jan 2017 01:00:35: 11000000
INFO @ Sun, 29 Jan 2017 01:00:35: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 01:00:35: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 01:00:35: #1 total tags in treatment: 9093642
INFO @ Sun, 29 Jan 2017 01:00:35: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 01:00:35: #1 finished!
INFO @ Sun, 29 Jan 2017 01:00:35: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 01:00:35: #2 Skipped...
INFO @ Sun, 29 Jan 2017 01:00:35: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 01:00:35: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 01:00:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 01:00:35: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 01:01:22: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 01:02:37: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 01:02:45: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 01:02:50: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 01:02:55: Done!
|
Num | 18 | ID | task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27 | Name | macs2 rep1-pr2 | Thread | thread_Root | PID | 36037 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 00:56:41 | End | 2017-01-29 01:03:02 | Elapsed | 00:06:21 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# SYS command. line 82
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
# SYS command. line 85
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 92
macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# SYS command. line 95
sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
# SYS command. line 96
sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
# SYS command. line 99
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed
# SYS command. line 110
if [[ false == "false" ]]; then \
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 124
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 125
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg
# SYS command. line 128
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 129
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
# SYS command. line 130
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 136
chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 138
controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 140
macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 143
slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 144
rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg
# SYS command. line 147
sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 148
bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
# SYS command. line 149
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 151
rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.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--------------------
27068 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
INFO @ Sun, 29 Jan 2017 00:56:54:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 00:56:54: #1 read tag files...
INFO @ Sun, 29 Jan 2017 00:56:54: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 00:56:55: 1000000
INFO @ Sun, 29 Jan 2017 00:56:57: 2000000
INFO @ Sun, 29 Jan 2017 00:56:59: 3000000
INFO @ Sun, 29 Jan 2017 00:57:00: 4000000
INFO @ Sun, 29 Jan 2017 00:57:02: 5000000
INFO @ Sun, 29 Jan 2017 00:57:03: 6000000
INFO @ Sun, 29 Jan 2017 00:57:05: 7000000
INFO @ Sun, 29 Jan 2017 00:57:06: 8000000
INFO @ Sun, 29 Jan 2017 00:57:08: 9000000
INFO @ Sun, 29 Jan 2017 00:57:08: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 00:57:10: 1000000
INFO @ Sun, 29 Jan 2017 00:57:11: 2000000
INFO @ Sun, 29 Jan 2017 00:57:12: 3000000
INFO @ Sun, 29 Jan 2017 00:57:14: 4000000
INFO @ Sun, 29 Jan 2017 00:57:15: 5000000
INFO @ Sun, 29 Jan 2017 00:57:17: 6000000
INFO @ Sun, 29 Jan 2017 00:57:18: 7000000
INFO @ Sun, 29 Jan 2017 00:57:19: 8000000
INFO @ Sun, 29 Jan 2017 00:57:21: 9000000
INFO @ Sun, 29 Jan 2017 00:57:22: 10000000
INFO @ Sun, 29 Jan 2017 00:57:24: 11000000
INFO @ Sun, 29 Jan 2017 00:57:24: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 00:57:24: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 00:57:24: #1 total tags in treatment: 9093642
INFO @ Sun, 29 Jan 2017 00:57:24: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 00:57:24: #1 finished!
INFO @ Sun, 29 Jan 2017 00:57:24: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 00:57:24: #2 Skipped...
INFO @ Sun, 29 Jan 2017 00:57:24: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 00:57:24: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 00:57:24: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Sun, 29 Jan 2017 00:57:24: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 00:58:12: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Sun, 29 Jan 2017 00:58:12: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg
INFO @ Sun, 29 Jan 2017 00:58:12: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg
INFO @ Sun, 29 Jan 2017 00:58:12: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Sun, 29 Jan 2017 00:58:12: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 00:59:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 00:59:57: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak
INFO @ Sun, 29 Jan 2017 00:59:58: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed
INFO @ Sun, 29 Jan 2017 00:59:59: Done!
INFO @ Sun, 29 Jan 2017 01:00:02:
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/align/ctl1/ENCFF001HNC.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 01:00:02: #1 read tag files...
INFO @ Sun, 29 Jan 2017 01:00:02: #1 read treatment tags...
INFO @ Sun, 29 Jan 2017 01:00:04: 1000000
INFO @ Sun, 29 Jan 2017 01:00:05: 2000000
INFO @ Sun, 29 Jan 2017 01:00:07: 3000000
INFO @ Sun, 29 Jan 2017 01:00:08: 4000000
INFO @ Sun, 29 Jan 2017 01:00:10: 5000000
INFO @ Sun, 29 Jan 2017 01:00:11: 6000000
INFO @ Sun, 29 Jan 2017 01:00:13: 7000000
INFO @ Sun, 29 Jan 2017 01:00:14: 8000000
INFO @ Sun, 29 Jan 2017 01:00:16: 9000000
INFO @ Sun, 29 Jan 2017 01:00:16: #1.2 read input tags...
INFO @ Sun, 29 Jan 2017 01:00:18: 1000000
INFO @ Sun, 29 Jan 2017 01:00:19: 2000000
INFO @ Sun, 29 Jan 2017 01:00:21: 3000000
INFO @ Sun, 29 Jan 2017 01:00:22: 4000000
INFO @ Sun, 29 Jan 2017 01:00:24: 5000000
INFO @ Sun, 29 Jan 2017 01:00:25: 6000000
INFO @ Sun, 29 Jan 2017 01:00:26: 7000000
INFO @ Sun, 29 Jan 2017 01:00:28: 8000000
INFO @ Sun, 29 Jan 2017 01:00:29: 9000000
INFO @ Sun, 29 Jan 2017 01:00:31: 10000000
INFO @ Sun, 29 Jan 2017 01:00:32: 11000000
INFO @ Sun, 29 Jan 2017 01:00:33: #1 tag size is determined as 50 bps
INFO @ Sun, 29 Jan 2017 01:00:33: #1 tag size = 50
INFO @ Sun, 29 Jan 2017 01:00:33: #1 total tags in treatment: 9093642
INFO @ Sun, 29 Jan 2017 01:00:33: #1 total tags in control: 11201413
INFO @ Sun, 29 Jan 2017 01:00:33: #1 finished!
INFO @ Sun, 29 Jan 2017 01:00:33: #2 Build Peak Model...
INFO @ Sun, 29 Jan 2017 01:00:33: #2 Skipped...
INFO @ Sun, 29 Jan 2017 01:00:33: #2 Use 100 as fragment length
INFO @ Sun, 29 Jan 2017 01:00:33: #3 Call peaks...
INFO @ Sun, 29 Jan 2017 01:00:33: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Sun, 29 Jan 2017 01:00:33: #3 Pre-compute pvalue-qvalue table...
INFO @ Sun, 29 Jan 2017 01:01:18: #3 Call peaks for each chromosome...
INFO @ Sun, 29 Jan 2017 01:02:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls
INFO @ Sun, 29 Jan 2017 01:02:38: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak
INFO @ Sun, 29 Jan 2017 01:02:42: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak
INFO @ Sun, 29 Jan 2017 01:02:47: Done!
|
Num | 19 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36053 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:20:32 | End | 2017-01-29 01:21:52 | Elapsed | 00:01:20 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
9577 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000225.1 50807 50985 Peak_82 342 . 16.22400 34.28613 28.49260 88
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000225.1 50807 50985 Peak_82 342 . 16.22400 34.28613 28.49260 88
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1 121462 121805 Peak_386 193 . 11.22081 19.34293 14.38472 107
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN538364.1 121462 121805 Peak_386 193 . 11.22081 19.34293 14.38472 107
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000216.2 144013 144149 Peak_5969 41 . 3.75388 4.13902 0.55912 76
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000216.2 144013 144149 Peak_5969 41 . 3.75388 4.13902 0.55912 76
|
Num | 20 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36054 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:20:33 | End | 2017-01-29 01:21:53 | Elapsed | 00:01:20 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
9576 (process ID) old priority 0, new priority 10
Waiting for 30 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270712.1 151017 151117 Peak_325 105 . 151017 151117 0 2 1,1 0,99 9.08261 14.96679 10.52660
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270712.1 151017 151117 Peak_325 105 . 151017 151117 0 2 1,1 0,99 9.08261 14.96679 10.52660
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1 92234 92334 Peak_583 70 . 92234 92334 0 2 1,1 0,99 7.48054 11.41882 7.02395
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1 92234 92334 Peak_583 70 . 92234 92334 0 2 1,1 0,99 7.48054 11.41882 7.02395
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000008.2 2537 4196 Peak_126627 0 . 2537 4196 0 3 1,121,1 0,434,1658 1.49487 1.08431 0.00000
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000008.2 2537 4196 Peak_126627 0 . 2537 4196 0 3 1,121,1 0,434,1658 1.49487 1.08431 0.00000
|
Num | 21 | ID | task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30 | Name | naive_overlap_thresh | Thread | thread_Root | PID | 36055 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:20:34 | End | 2017-01-29 01:21:52 | Elapsed | 00:01:18 | Timeout | 01:00:00 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
| Dependencies | | |
# SYS command. line 61
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 64
intersectBed -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1016004.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1016004.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
awk 'BEGIN{FS="\t";OFS="\t"} {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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz
# SYS command. line 70
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz
# SYS command. line 72
bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
# SYS command. line 74
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz
# SYS command. line 76
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
9578 (process ID) old priority 0, new priority 10
Waiting for 38 seconds.
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270712.1 151017 151117 Peak_325 105 . 9.08261 14.96679 10.52660
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270712.1 151017 151117 Peak_325 105 . 9.08261 14.96679 10.52660
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1 92234 92334 Peak_583 70 . 7.48054 11.41882 7.02395
***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270772.1 92234 92334 Peak_583 70 . 7.48054 11.41882 7.02395
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000008.2 2537 4196 Peak_126627 0 . 1.49487 1.08431 0.00000
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000008.2 2537 4196 Peak_126627 0 . 1.49487 1.08431 0.00000
|
Num | 22 | ID | task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31 | Name | blacklist_filter peak 1 | Thread | thread_Root | PID | 3329 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:21:55 | End | 2017-01-29 01:23:03 | Elapsed | 00:01:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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 $0}' \
| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
# SYS command. line 35
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
3334 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000225.1 50811 50987 Peak_184 288 . 13.95095 28.80012 23.44261 84
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/rep1/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
GL000225.1 50811 50987 Peak_184 288 . 13.95095 28.80012 23.44261 84
|
Num | 23 | ID | task.report.peak2hammock.line_412.id_32 | Name | peak2hammock | Thread | thread_Root | PID | 7356 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:23:04 | End | 2017-01-29 01:23:13 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
--------------------Stdout--------------------
7361 (process ID) old priority 0, new priority 10
|
Num | 24 | ID | task.report.peak2hammock.line_412.id_33 | Name | peak2hammock | Thread | thread_Root | PID | 7977 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:23:14 | End | 2017-01-29 01:23:36 | Elapsed | 00:00:21 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.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/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock
# SYS command. line 418
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/peak/macs2/overlap/SRR1016004.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
--------------------Stdout--------------------
7981 (process ID) old priority 0, new priority 10
|
Num | 25 | ID | task.graphviz.report.line_97.id_34 | Name | report | Thread | thread_Root | PID | 9360 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:23:36 | End | 2017-01-29 01:23:45 | 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 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/report/EP300_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/report/EP300_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/report/EP300_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout--------------------
9366 (process ID) old priority 0, new priority 10
|
Num | 26 | ID | task.report.pdf2png.line_379.id_39 | Name | pdf2png | Thread | thread_Root | PID | 9367 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | | Mem | | | Start | 2017-01-29 01:23:37 | End | 2017-01-29 01:23:45 | Elapsed | 00:00:08 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.pdf
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.png
| Dependencies | | |
# SYS command. line 380
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# 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/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/EP300/out/qc/rep1/SRR1016004.nodup.15M.cc.plot.pdf
--------------------Stdout--------------------
9379 (process ID) old priority 0, new priority 10
|