| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161201_195429_747 |
| Start time | 2016-12-01 19:54:29 |
| Run time | 02:19:45.615 |
| Tasks executed | 11 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-title, SI0428, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20161201_195429_747/task.graphviz.report.line_97.id_19 chipseq.bds.20161201_195429_747/task.report.pdf2png.line_324.id_22 |
| thread_41 | thread_Root | chipseq.bds.20161201_195429_747_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161201_195429_747_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_12 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_13 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_14 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_15 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_16 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bed.spr_rep1.line_255.id_17 chipseq.bds.20161201_195429_747_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_18 |
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# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 113
bwa aln -q 5 -l 32 -k 2 -t 5 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.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-------------------- 15818 (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] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.85 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.30 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.44 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.68 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.06 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.87 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.11 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.83 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.31 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.62 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.35 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.97 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.72 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.39 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.33 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.29 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.93 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.82 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.82 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.04 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.49 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.76 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.13 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.96 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.02 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.15 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.99 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.95 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.59 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.07 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18296411 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 5 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz [main] Real time: 603.447 sec; CPU: 2659.876 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 5 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.bam
# SYS command. line 149
sambamba flagstat -t 5 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 16701 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.44 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 0.78 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.24 sec [bwa_aln_core] refine gapped alignments... 5.34 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.02 sec [bwa_aln_core] refine gapped alignments... 4.99 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.70 sec [bwa_aln_core] refine gapped alignments... 5.33 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.81 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.59 sec [bwa_aln_core] refine gapped alignments... 4.46 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.85 sec [bwa_aln_core] refine gapped alignments... 4.74 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.28 sec [bwa_aln_core] refine gapped alignments... 4.87 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.72 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.55 sec [bwa_aln_core] refine gapped alignments... 2.93 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.35 sec [bwa_aln_core] refine gapped alignments... 1.87 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.76 sec [bwa_aln_core] refine gapped alignments... 1.76 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.93 sec [bwa_aln_core] refine gapped alignments... 2.18 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.31 sec [bwa_aln_core] refine gapped alignments... 2.48 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.27 sec [bwa_aln_core] refine gapped alignments... 2.84 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.96 sec [bwa_aln_core] refine gapped alignments... 3.14 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 87.01 sec [bwa_aln_core] refine gapped alignments... 6.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.49 sec [bwa_aln_core] refine gapped alignments... 3.58 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.81 sec [bwa_aln_core] refine gapped alignments... 3.91 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.19 sec [bwa_aln_core] refine gapped alignments... 6.33 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.83 sec [bwa_aln_core] refine gapped alignments... 4.65 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.05 sec [bwa_aln_core] refine gapped alignments... 4.93 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.92 sec [bwa_aln_core] refine gapped alignments... 5.03 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.12 sec [bwa_aln_core] refine gapped alignments... 5.11 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 53.50 sec [bwa_aln_core] refine gapped alignments... 6.59 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.22 sec [bwa_aln_core] refine gapped alignments... 4.67 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.91 sec [bwa_aln_core] refine gapped alignments... 7.09 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.31 sec [bwa_aln_core] refine gapped alignments... 4.96 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.11 sec [bwa_aln_core] refine gapped alignments... 5.04 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.93 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.14 sec [bwa_aln_core] refine gapped alignments... 4.65 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 123.34 sec [bwa_aln_core] refine gapped alignments... 24.34 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 132.86 sec [bwa_aln_core] refine gapped alignments... 16.86 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 161.58 sec [bwa_aln_core] refine gapped alignments... 22.36 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 164.27 sec [bwa_aln_core] refine gapped alignments... 29.80 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 139.78 sec [bwa_aln_core] refine gapped alignments... 27.96 sec [bwa_aln_core] print alignments... 0.80 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 128.45 sec [bwa_aln_core] refine gapped alignments... 21.88 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 140.47 sec [bwa_aln_core] refine gapped alignments... 29.27 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 165.67 sec [bwa_aln_core] refine gapped alignments... 22.23 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 152.66 sec [bwa_aln_core] refine gapped alignments... 29.12 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 134.08 sec [bwa_aln_core] refine gapped alignments... 40.41 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 141.70 sec [bwa_aln_core] refine gapped alignments... 26.00 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 162.72 sec [bwa_aln_core] refine gapped alignments... 19.64 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 150.84 sec [bwa_aln_core] refine gapped alignments... 23.01 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 164.13 sec [bwa_aln_core] refine gapped alignments... 24.87 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 150.29 sec [bwa_aln_core] refine gapped alignments... 29.84 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 159.93 sec [bwa_aln_core] refine gapped alignments... 23.01 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 137.67 sec [bwa_aln_core] refine gapped alignments... 23.09 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 128.25 sec [bwa_aln_core] refine gapped alignments... 18.46 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 129.84 sec [bwa_aln_core] refine gapped alignments... 22.74 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 133.63 sec [bwa_aln_core] refine gapped alignments... 22.10 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 124.37 sec [bwa_aln_core] refine gapped alignments... 10.33 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.48 sec [bwa_aln_core] refine gapped alignments... 6.90 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.12 sec [bwa_aln_core] refine gapped alignments... 5.05 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.11 sec [bwa_aln_core] refine gapped alignments... 4.88 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.94 sec [bwa_aln_core] refine gapped alignments... 5.05 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.09 sec [bwa_aln_core] refine gapped alignments... 25.75 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 126.94 sec [bwa_aln_core] refine gapped alignments... 22.94 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 127.83 sec [bwa_aln_core] refine gapped alignments... 23.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 132.43 sec [bwa_aln_core] refine gapped alignments... 21.98 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 133.01 sec [bwa_aln_core] refine gapped alignments... 20.88 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 131.63 sec [bwa_aln_core] refine gapped alignments... 24.23 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 123.28 sec [bwa_aln_core] refine gapped alignments... 23.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 115.24 sec [bwa_aln_core] refine gapped alignments... 26.00 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 135.73 sec [bwa_aln_core] refine gapped alignments... 8.92 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.29 sec [bwa_aln_core] refine gapped alignments... 7.09 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.52 sec [bwa_aln_core] refine gapped alignments... 7.09 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.46 sec [bwa_aln_core] refine gapped alignments... 8.24 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.63 sec [bwa_aln_core] refine gapped alignments... 6.63 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.28 sec [bwa_aln_core] refine gapped alignments... 6.73 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18296411 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz [main] Real time: 6551.157 sec; CPU: 6508.712 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 5 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 5 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.bam | \
sambamba sort -t 5 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.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-------------------- 52818 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 17975 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Dec 01 21:57:05 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Dec 01 21:57:05 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-12-01 21:57:05 MarkDuplicates Start of doWork freeMemory: 254879312; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-12-01 21:57:05 MarkDuplicates Reading input file and constructing read end information. INFO 2016-12-01 21:57:05 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-12-01 21:57:11 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:185,977,689 INFO 2016-12-01 21:57:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:16 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 4s. Last read position: chr2:142,196,718 INFO 2016-12-01 21:57:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:20 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 4s. Last read position: chr3:120,120,962 INFO 2016-12-01 21:57:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:24 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 4s. Last read position: chr4:150,141,593 INFO 2016-12-01 21:57:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:28 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr5:132,500,316 INFO 2016-12-01 21:57:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:32 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr6:116,651,017 INFO 2016-12-01 21:57:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:36 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 4s. Last read position: chr7:144,813,689 INFO 2016-12-01 21:57:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:42 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 6s. Last read position: chr9:90,991,217 INFO 2016-12-01 21:57:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:47 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 4s. Last read position: chr10:130,349,720 INFO 2016-12-01 21:57:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:51 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr12:77,313,724 INFO 2016-12-01 21:57:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:57:57 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 6s. Last read position: chr14:50,756,963 INFO 2016-12-01 21:57:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:58:01 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr16:74,433,256 INFO 2016-12-01 21:58:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:58:04 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr19:13,405,359 INFO 2016-12-01 21:58:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:58:13 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 8s. Last read position: chr22:41,231,834 INFO 2016-12-01 21:58:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:58:17 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 4s. Last read position: chrX:147,957,210 INFO 2016-12-01 21:58:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-12-01 21:58:18 MarkDuplicates Read 15073863 records. 0 pairs never matched. INFO 2016-12-01 21:58:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 2553127712; totalMemory: 3912761344; maxMemory: 11453595648 INFO 2016-12-01 21:58:25 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-12-01 21:58:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-12-01 21:58:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-12-01 21:58:56 MarkDuplicates Sorting list of duplicate records. INFO 2016-12-01 21:58:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 3870599696; totalMemory: 6776422400; maxMemory: 11453595648 INFO 2016-12-01 21:58:59 MarkDuplicates Marking 4141 records as duplicates. INFO 2016-12-01 21:58:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-12-01 22:00:37 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 97s. Last read position: chr12:77,313,724 INFO 2016-12-01 22:01:28 MarkDuplicates Before output close freeMemory: 7194488072; totalMemory: 7249330176; maxMemory: 11453595648 INFO 2016-12-01 22:01:28 MarkDuplicates After output close freeMemory: 6783445120; totalMemory: 6838288384; maxMemory: 11453595648 [Thu Dec 01 22:01:28 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.39 minutes. Runtime.totalMemory()=6838288384 | ||||||||||||||||||||||||||||||||||||||||
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# 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/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.bam
# SYS command. line 153
sambamba index -t 5 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.bam
# SYS command. line 155
sambamba flagstat -t 5 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.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/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.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-------------------- 6344 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# 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/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 53087 (process ID) old priority 0, new priority 10 Waiting for 27 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# 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 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 53182 (process ID) old priority 0, new priority 10 Waiting for 35 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr2/SI0428.nodup.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/pseudo_reps/rep1/pr1/SI0428.nodup.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 53181 (process ID) old priority 0, new priority 10 Waiting for 29 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# 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/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.15M.tagAlign.gz -p=5 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.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--------------------
17287 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.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: 5
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/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/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/align/rep1/SI0428.nodup.nodup.15M.tagAlign.gz
opened /tmp/16261.1.q/RtmpBxgRtZ/SI0428.nodup.nodup.15M.tagAlign43c72bc1bd02
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1736207
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.186594298402653,0.174693099513519,0.174389354508296
Top 3 estimates for fragment length 145,215,250
Window half size 185
Phantom peak location 50
Phantom peak Correlation 0.1755556
Normalized Strand cross-correlation coefficient (NSC) 1.074724
Relative Strand cross-correlation Coefficient (RSC) 6.70482
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
Loading required package: caTools
| ||||||||||||||||||||||||||||||||||||||||
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# 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/HughesZnfData/hg19BamFiles/SI0428/out/report/SI0428_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/report/SI0428_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/report/SI0428_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 53415 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 325
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 326
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/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out/qc/rep1/SI0428.nodup.nodup.15M.cc.plot.pdf
--------------------Stdout-------------------- 53443 (process ID) old priority 0, new priority 10 |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, SI0428, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428.nodup.fastq.gz, -final_stage, xcor, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DERBY_HOME | /usr/lib/jvm/java-8-oracle/db |
| string | DISPLAY | localhost:11.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| string | J2REDIR | /usr/lib/jvm/java-8-oracle/jre |
| string | J2SDKDIR | /usr/lib/jvm/java-8-oracle |
| string | JAVA_HOME | /usr/lib/jvm/java-8-oracle |
| int | K | 1024 |
| string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_PyTBeB |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5 |
| string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/hg19BamFiles/SI0428 |
| string | PYTHONPATH | /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 50523 22 |
| string | SSH_CONNECTION | 171.65.77.8 50523 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/5 |
| string | STY | 39293.SI0428.BDS |
| string | system | sge |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
| int | timeout | -1 |
| string | USER | imk1 |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1048 |
| string | XDG_SESSION_ID | 1286 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |