| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161109_175121_699 |
| Start time | 2016-11-09 17:51:21 |
| Run time | 3 days 19:15:44.508 |
| Tasks executed | 4 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 bwa_sam rep1 |
| Arguments* | [-title, SRR1370889_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370889_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_42 | thread_Root | chipseq.bds.20161109_175121_699_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161109_175121_699_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12 |
| thread_41 | thread_Root | chipseq.bds.20161109_175121_699_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161109_175121_699_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 113
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370889_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/rep1/SRR1370889_1.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 51675 (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] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.50 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.83 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.09 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.95 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.12 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.68 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.28 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.16 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.10 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.37 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.53 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.42 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.34 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.51 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.86 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.25 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.22 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.38 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.03 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.35 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.37 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.24 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.65 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.45 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.82 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.20 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.07 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.12 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.19 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.53 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.03 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.14 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.46 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.52 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21735373 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370889_1.fastq.gz [main] Real time: 5469.090 sec; CPU: 5415.280 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21948 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
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 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 4592 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Nov 09 21:20:15 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Nov 09 21:20:15 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-09 21:20:15 MarkDuplicates Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-11-09 21:20:15 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-09 21:20:15 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-11-09 21:20:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 16s. Last read position: chr1:22,298,551 INFO 2016-11-09 21:20:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:20:45 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 11s. Last read position: chr1:41,895,424 INFO 2016-11-09 21:20:45 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-09 21:20:55 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 9s. Last read position: chr1:63,396,527 INFO 2016-11-09 21:20:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-09 21:21:03 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 8s. Last read position: chr1:89,147,707 INFO 2016-11-09 21:21:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:21:09 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 6s. Last read position: chr1:115,615,553 INFO 2016-11-09 21:21:09 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:21:16 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 6s. Last read position: chr1:164,468,682 INFO 2016-11-09 21:21:16 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-09 21:21:22 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 6s. Last read position: chr1:189,102,252 INFO 2016-11-09 21:21:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-09 21:21:32 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 9s. Last read position: chr1:213,979,760 INFO 2016-11-09 21:21:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:21:38 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 6s. Last read position: chr1:231,814,268 INFO 2016-11-09 21:21:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:21:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 6s. Last read position: chr2:3,652,468 INFO 2016-11-09 21:21:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-09 21:21:52 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 7s. Last read position: chr2:39,505,122 INFO 2016-11-09 21:21:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:21:58 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 5s. Last read position: chr2:73,561,393 INFO 2016-11-09 21:21:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-09 21:22:05 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 7s. Last read position: chr2:120,526,571 INFO 2016-11-09 21:22:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:22:12 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 6s. Last read position: chr2:160,316,783 INFO 2016-11-09 21:22:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:22:35 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 22s. Last read position: chr2:195,549,735 INFO 2016-11-09 21:22:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:22:43 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 7s. Last read position: chr2:230,358,034 INFO 2016-11-09 21:22:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-09 21:22:48 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 5s. Last read position: chr3:16,305,780 INFO 2016-11-09 21:22:48 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-09 21:22:54 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 5s. Last read position: chr3:49,251,279 INFO 2016-11-09 21:22:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:23:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 7s. Last read position: chr3:84,621,225 INFO 2016-11-09 21:23:01 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:23:08 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 6s. Last read position: chr3:128,121,129 INFO 2016-11-09 21:23:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:23:16 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 7s. Last read position: chr3:165,373,238 INFO 2016-11-09 21:23:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:23:25 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 9s. Last read position: chr3:195,333,247 INFO 2016-11-09 21:23:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:23:32 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 6s. Last read position: chr4:37,752,582 INFO 2016-11-09 21:23:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-09 21:23:40 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 8s. Last read position: chr4:81,286,306 INFO 2016-11-09 21:23:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:23:50 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 10s. Last read position: chr4:119,339,736 INFO 2016-11-09 21:23:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-09 21:23:57 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 6s. Last read po | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/rep1/SRR1370889_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370889_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/rep1/SRR1370889_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/align/rep1/SRR1370889_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370889_1/out/qc/rep1/SRR1370889_1.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
|
| Type | Name | Value |
|---|---|---|
| int{} | filesize | {rep1=3263723208, ctl1=11033042636} |
| int{} | nth_rep | {rep1=1, ctl1=4} |