| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_171017_013 |
| Start time | 2016-11-10 17:10:17 |
| Run time | 05:37:38.416 |
| Tasks executed | 12 |
| Tasks failed | 1 |
| Tasks failed names | markdup_bam_picard ctl1 |
| Arguments* | [-title, SRR1370892_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370892_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 | chipseq.bds.20161110_171017_013/task.graphviz.report.line_97.id_20 chipseq.bds.20161110_171017_013/task.report.pdf2png.line_324.id_23 |
| thread_41 | thread_Root | chipseq.bds.20161110_171017_013_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_13 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_15 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_16 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_17 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bed.spr_rep1.line_255.id_18 chipseq.bds.20161110_171017_013_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_19 |
| thread_42 | thread_Root | chipseq.bds.20161110_171017_013_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_171017_013_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 |
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_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/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_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/SRR1370892_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-------------------- 11498 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370892_1/out/align/rep1/SRR1370892_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370892_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 11500 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.12 sec [bwa_aln_core] refine gapped alignments... 1.33 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 1.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.29 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.90 sec [bwa_aln_core] refine gapped alignments... 2.58 sec [bwa_aln_core] print alignments... 1.07 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.61 sec [bwa_aln_core] refine gapped alignments... 2.61 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.04 sec [bwa_aln_core] refine gapped alignments... 2.48 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.56 sec [bwa_aln_core] refine gapped alignments... 2.54 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.85 sec [bwa_aln_core] refine gapped alignments... 2.56 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.27 sec [bwa_aln_core] refine gapped alignments... 2.61 sec [bwa_aln_core] print alignments... 1.26 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.38 sec [bwa_aln_core] refine gapped alignments... 2.58 sec [bwa_aln_core] print alignments... 1.18 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.83 sec [bwa_aln_core] refine gapped alignments... 2.65 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.67 sec [bwa_aln_core] refine gapped alignments... 2.48 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.91 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 1.21 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.07 sec [bwa_aln_core] refine gapped alignments... 2.39 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.69 sec [bwa_aln_core] refine gapped alignments... 2.45 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.36 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 1.14 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.41 sec [bwa_aln_core] refine gapped alignments... 2.26 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.60 sec [bwa_aln_core] refine gapped alignments... 2.36 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.25 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.23 sec [bwa_aln_core] refine gapped alignments... 2.07 sec [bwa_aln_core] print alignments... 1.18 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.29 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.17 sec [bwa_aln_core] refine gapped alignments... 2.23 sec [bwa_aln_core] print alignments... 1.25 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.80 sec [bwa_aln_core] refine gapped alignments... 2.33 sec [bwa_aln_core] print alignments... 1.17 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.44 sec [bwa_aln_core] refine gapped alignments... 2.08 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.62 sec [bwa_aln_core] refine gapped alignments... 2.01 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.58 sec [bwa_aln_core] refine gapped alignments... 2.11 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.85 sec [bwa_aln_core] refine gapped alignments... 2.46 sec [bwa_aln_core] print alignments... 1.21 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.44 sec [bwa_aln_core] refine gapped alignments... 2.36 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.22 sec [bwa_aln_core] refine gapped alignments... 2.22 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.87 sec [bwa_aln_core] refine gapped alignments... 2.28 sec [bwa_aln_core] print alignments... 1.14 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.85 sec [bwa_aln_core] refine gapped alignments... 2.06 sec [bwa_aln_core] print alignments... 1.06 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.95 sec [bwa_aln_core] refine gapped alignments... 2.24 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.01 sec [bwa_aln_core] refine gapped alignments... 2.30 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.09 sec [bwa_aln_core] refine gapped alignments... 2.72 sec [bwa_aln_core] print alignments... 1.18 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.31 sec [bwa_aln_core] refine gapped alignments... 2.38 sec [bwa_aln_core] print alignments... 1.17 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.45 sec [bwa_aln_core] refine gapped alignments... 1.86 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.65 sec [bwa_aln_core] refine gapped alignments... 2.05 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.64 sec [bwa_aln_core] refine gapped alignments... 2.14 sec [bwa_aln_core] print alignments... 1.10 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.76 sec [bwa_aln_core] refine gapped alignments... 1.90 sec [bwa_aln_core] print alignments... 1.41 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.06 sec [bwa_aln_core] refine gapped alignments... 2.13 sec [bwa_aln_core] print alignments... 1.25 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.67 sec [bwa_aln_core] refine gapped alignments... 2.03 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.24 sec [bwa_aln_core] refine gapped alignments... 2.65 sec [bwa_aln_core] print alignments... 1.26 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.46 sec [bwa_aln_core] refine gapped alignments... 1.80 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.75 sec [bwa_aln_core] refine gapped alignments... 2.69 sec [bwa_aln_core] print alignments... 1.17 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.75 sec [bwa_aln_core] refine gapped alignments... 1.94 sec [bwa_aln_core] print alignments... 1.15 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.50 sec [bwa_aln_core] refine gapped alignments... 2.37 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.74 sec [bwa_aln_core] refine gapped alignments... 1.80 sec [bwa_aln_core] print alignments... 1.13 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.65 sec [bwa_aln_core] refine gapped alignments... 2.05 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.07 sec [bwa_aln_core] refine gapped alignments... 2.71 sec [bwa_aln_core] print alignments... 1.18 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.01 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 1.16 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.21 sec [bwa_aln_core] refine gapped alignments... 2.73 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.24 sec [bwa_aln_core] refine gapped alignments... 2.75 sec [bwa_aln_core] print alignments... 1.18 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.38 sec [bwa_aln_core] refine gapped alignments... 2.62 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.11 sec [bwa_aln_core] refine gapped alignments... 2.78 sec [bwa_aln_core] print alignments... 1.30 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.17 sec [bwa_aln_core] refine gapped alignments... 2.73 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.03 sec [bwa_aln_core] refine gapped alignments... 2.68 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.42 sec [bwa_aln_core] refine gapped alignments... 2.59 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.45 sec [bwa_aln_core] refine gapped alignments... 2.61 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.65 sec [bwa_aln_core] refine gapped alignments... 2.71 sec [bwa_aln_core] print alignments... 1.27 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.51 sec [bwa_aln_core] refine gapped alignments... 2.75 sec [bwa_aln_core] print alignments... 1.26 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.28 sec [bwa_aln_core] refine gapped alignments... 2.78 sec [bwa_aln_core] print alignments... 1.42 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.83 sec [bwa_aln_core] refine gapped alignments... 2.77 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.16 sec [bwa_aln_core] refine gapped alignments... 2.77 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.14 sec [bwa_aln_core] refine gapped alignments... 2.90 sec [bwa_aln_core] print alignments... 1.38 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.56 sec [bwa_aln_core] refine gapped alignments... 2.87 sec [bwa_aln_core] print alignments... 1.25 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.47 sec [bwa_aln_core] refine gapped alignments... 2.70 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.23 sec [bwa_aln_core] refine gapped alignments... 2.93 sec [bwa_aln_core] print alignments... 1.49 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.58 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 1.21 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.97 sec [bwa_aln_core] refine gapped alignments... 2.62 sec [bwa_aln_core] print alignments... 1.22 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.03 sec [bwa_aln_core] refine gapped alignments... 2.70 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.02 sec [bwa_aln_core] refine gapped alignments... 2.78 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.76 sec [bwa_aln_core] refine gapped alignments... 2.68 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.88 sec [bwa_aln_core] refine gapped alignments... 2.74 sec [bwa_aln_core] print alignments... 1.20 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.78 sec [bwa_aln_core] refine gapped alignments... 2.63 sec [bwa_aln_core] print alignments... 1.24 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.39 sec [bwa_aln_core] refine gapped alignments... 2.58 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.61 sec [bwa_aln_core] refine gapped alignments... 2.75 sec [bwa_aln_core] print alignments... 1.19 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.59 sec [bwa_aln_core] refine gapped alignments... 2.69 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.35 sec [bwa_aln_core] refine gapped alignments... 2.67 sec [bwa_aln_core] print alignments... 1.23 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.86 sec [bwa_aln_core] refine gapped alignments... 2.77 sec [bwa_aln_core] print alignments... 1.21 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.43 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.13 sec [bwa_aln_core] 20475378 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/SRR1370892_1/out/align/rep1/SRR1370892_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370892_1.fastq.gz [main] Real time: 1955.466 sec; CPU: 1643.688 sec | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_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/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19669 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 20:01:06 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 20:01:06 PST 2016] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-10 20:01:26 MarkDuplicates Start of doWork freeMemory: 254877736; totalMemory: 257425408; maxMemory: 11453595648
INFO 2016-11-10 20:01:26 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-10 20:01:26 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
INFO 2016-11-10 20:02:31 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 35s. Last read position: chr1:22,298,551
INFO 2016-11-10 20:02:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:02:50 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 19s. Last read position: chr1:41,895,424
INFO 2016-11-10 20:02:50 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:03:20 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 29s. Last read position: chr1:63,396,527
INFO 2016-11-10 20:03:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:03:53 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 32s. Last read position: chr1:89,147,707
INFO 2016-11-10 20:03:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:04:27 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 34s. Last read position: chr1:115,615,553
INFO 2016-11-10 20:04:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:05:23 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 56s. Last read position: chr1:164,468,682
INFO 2016-11-10 20:05:23 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:06:11 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 47s. Last read position: chr1:189,102,252
INFO 2016-11-10 20:06:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:06:43 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 32s. Last read position: chr1:213,979,760
INFO 2016-11-10 20:06:43 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:07:26 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 42s. Last read position: chr1:231,814,268
INFO 2016-11-10 20:07:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:08:12 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 46s. Last read position: chr2:3,652,468
INFO 2016-11-10 20:08:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:09:11 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 58s. Last read position: chr2:39,505,122
INFO 2016-11-10 20:09:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:10:07 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 55s. Last read position: chr2:73,561,393
INFO 2016-11-10 20:10:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:10:55 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 48s. Last read position: chr2:120,526,571
INFO 2016-11-10 20:10:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:11:38 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 43s. Last read position: chr2:160,316,783
INFO 2016-11-10 20:11:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:12:22 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 43s. Last read position: chr2:195,549,735
INFO 2016-11-10 20:12:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:13:51 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 88s. Last read position: chr2:230,358,034
INFO 2016-11-10 20:13:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:14:31 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 39s. Last read position: chr3:16,305,780
INFO 2016-11-10 20:14:31 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:15:21 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 50s. Last read position: chr3:49,251,279
INFO 2016-11-10 20:15:21 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:15:49 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 27s. Last read position: chr3:84,621,225
INFO 2016-11-10 20:15:49 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:16:23 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 33s. Last read position: chr3:128,121,129
INFO 2016-11-10 20:16:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:16:56 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 33s. Last read position: chr3:165,373,238
INFO 2016-11-10 20:16:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:17:40 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 44s. Last read position: chr3:195,333,247
INFO 2016-11-10 20:17:40 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:18:24 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 44s. Last read position: chr4:37,752,582
INFO 2016-11-10 20:18:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:19:06 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:17:10s. Time for last 1,000,000: 41s. Last read position: chr4:81,286,306
INFO 2016-11-10 20:19:06 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:19:44 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:17:48s. Time for last 1,000,000: 38s. Last read position: chr4:119,339,736
INFO 2016-11-10 20:19:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:20:45 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 60s. Last read position: chr4:158,818,783
INFO 2016-11-10 20:20:45 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:23:28 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:21:32s. Time for last 1,000,000: 162s. Last read position: chr5:6,447,551
INFO 2016-11-10 20:23:28 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-10 20:24:51 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:22:55s. Time for last 1,000,000: 83s. Last read position: chr5:33,219,021
INFO 2016-11-10 20:24:51 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:26:08 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:24:12s. Time for last 1,000,000: 77s. Last read position: chr5:60,694,078
INFO 2016-11-10 20:26:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:27:15 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:25:19s. Time for last 1,000,000: 67s. Last read position: chr5:86,336,676
INFO 2016-11-10 20:27:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:28:08 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:26:12s. Time for last 1,000,000: 52s. Last read position: chr5:112,930,184
INFO 2016-11-10 20:28:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:29:37 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:27:41s. Time for last 1,000,000: 88s. Last read position: chr5:136,852,889
INFO 2016-11-10 20:29:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:32:16 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:30:20s. Time for last 1,000,000: 159s. Last read position: chr5:160,271,193
INFO 2016-11-10 20:32:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:33:20 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:31:24s. Time for last 1,000,000: 63s. Last read position: chr6:4,126,386
INFO 2016-11-10 20:33:20 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:36:46 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:34:50s. Time for last 1,000,000: 206s. Last read position: chr6:28,666,579
INFO 2016-11-10 20:36:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:39:03 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:37:07s. Time for last 1,000,000: 136s. Last read position: chr6:49,527,281
INFO 2016-11-10 20:39:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:40:29 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:38:33s. Time for last 1,000,000: 86s. Last read position: chr6:81,728,195
INFO 2016-11-10 20:40:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:46:13 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:44:17s. Time for last 1,000,000: 344s. Last read position: chr6:107,535,760
INFO 2016-11-10 20:46:13 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:47:53 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:45:57s. Time for last 1,000,000: 99s. Last read position: chr6:132,364,408
INFO 2016-11-10 20:47:53 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:53:21 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:51:25s. Time for last 1,000,000: 328s. Last read position: chr6:156,918,595
INFO 2016-11-10 20:53:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:57:33 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:55:37s. Time for last 1,000,000: 251s. Last read position: chr7:18,636,743
INFO 2016-11-10 20:57:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:01:04 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:59:08s. Time for last 1,000,000: 210s. Last read position: chr7:53,850,313
INFO 2016-11-10 21:01:04 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:07:27 MarkDuplicates Read 43,000,000 records. Elapsed time: 01:05:31s. Time for last 1,000,000: 383s. Last read position: chr7:96,503,433
INFO 2016-11-10 21:07:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 21:09:12 MarkDuplicates Read 44,000,000 records. Elapsed time: 01:07:16s. Time for last 1,000,000: 105s. Last read position: chr7:120,651,846
INFO 2016-11-10 21:09:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:12:05 MarkDuplicates Read 45,000,000 records. Elapsed time: 01:10:09s. Time for last 1,000,000: 172s. Last read position: chr7:146,401,497
INFO 2016-11-10 21:12:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:16:29 MarkDuplicates Read 46,000,000 records. Elapsed time: 01:14:33s. Time for last 1,000,000: 263s. Last read position: chr8:17,030,519
INFO 2016-11-10 21:16:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:17:48 MarkDuplicates Read 47,000,000 records. Elapsed time: 01:15:52s. Time for last 1,000,000: 79s. Last read position: chr8:42,750,671
INFO 2016-11-10 21:17:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:20:48 MarkDuplicates Read 48,000,000 records. Elapsed time: 01:18:52s. Time for last 1,000,000: 180s. Last read position: chr8:85,385,487
INFO 2016-11-10 21:20:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:22:42 MarkDuplicates Read 49,000,000 records. Elapsed time: 01:20:46s. Time for last 1,000,000: 113s. Last read position: chr8:124,358,985
INFO 2016-11-10 21:22:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 21:23:42 MarkDuplicates Read 50,000,000 records. Elapsed time: 01:21:46s. Time for last 1,000,000: 59s. Last read position: chr9:18,183,883
INFO 2016-11-10 21:23:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
/users/imk1/anaconda2/envs/aquas_chipseq/bin/picard: line 60: 21187 Killed java -Xms512m -Xmx1g -jar /users/imk1/anaconda2/envs/aquas_chipseq/share/picard-1.126-4/picard.jar MarkDuplicates INPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=false
--------------------Post mortem info--------------------
==============================================================
job_number: 7174
exec_file: job_scripts/7174
submission_time: Thu Nov 10 17:53:36 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/ascp/:/software/sratoolkit/2.5.2/bin/:/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
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/chipseq.bds.20161110_171017_013_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/chipseq.bds.20161110_171017_013_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=30759.SRR1370892_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
parallel environment: shm range: 1
usage 1: cpu=00:13:21, mem=2704.17102 GBs, io=11.96583, vmem=27.254M, maxvmem=3.451G
scheduling info: queue instance "amd.q@wotan" dropped because it is full
queue instance "q@kadru" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@surya" dropped because it is full
All queues dropped because of overload or full
| ||||||||||||||||||||||||||||||||||||||||
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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 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 19925 (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/SRR1370892_1/out/align/rep1/SRR1370892_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.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-------------------- 20134 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 21:33:28 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Nov 10 21:33:28 PST 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 21:33:38 MarkDuplicates Start of doWork freeMemory: 254879472; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 21:33:38 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 21:33:38 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 21:33:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:159,229,356 INFO 2016-11-10 21:33:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:05 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 7s. Last read position: chr2:55,134,217 INFO 2016-11-10 21:34:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:14 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 8s. Last read position: chr3:20,590,263 INFO 2016-11-10 21:34:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:21 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 6s. Last read position: chr4:22,555,573 INFO 2016-11-10 21:34:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:31 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 10s. Last read position: chr5:36,874,447 INFO 2016-11-10 21:34:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:36 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 4s. Last read position: chr5:178,975,675 INFO 2016-11-10 21:34:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:34:52 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 16s. Last read position: chr6:144,013,132 INFO 2016-11-10 21:34:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:02 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 9s. Last read position: chr7:151,093,837 INFO 2016-11-10 21:35:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:13 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 11s. Last read position: chr9:72,595,275 INFO 2016-11-10 21:35:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:17 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 4s. Last read position: chr10:95,971,069 INFO 2016-11-10 21:35:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:26 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 8s. Last read position: chr12:7,536,596 INFO 2016-11-10 21:35:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: chr13:41,398,329 INFO 2016-11-10 21:35:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:35 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 6s. Last read position: chr15:51,972,877 INFO 2016-11-10 21:35:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:42 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 6s. Last read position: chr17:18,818,192 INFO 2016-11-10 21:35:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 13s. Last read position: chr19:18,474,294 INFO 2016-11-10 21:35:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:35:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: chr22:20,794,177 INFO 2016-11-10 21:35:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:36:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 4s. Last read position: chrX:118,167,454 INFO 2016-11-10 21:36:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:36:05 MarkDuplicates Read 17318903 records. 0 pairs never matched. INFO 2016-11-10 21:36:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 4099248296; totalMemory: 5640290304; maxMemory: 11453595648 INFO 2016-11-10 21:36:09 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 21:36:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 21:36:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 21:36:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 21:36:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 2698600936; totalMemory: 5640290304; maxMemory: 11453595648 INFO 2016-11-10 21:36:12 MarkDuplicates Marking 446945 records as duplicates. INFO 2016-11-10 21:36:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-10 21:38:32 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 139s. Last read position: chr10:95,971,069 INFO 2016-11-10 21:40:00 MarkDuplicates Before output close freeMemory: 8301598184; totalMemory: 8382840832; maxMemory: 11453595648 INFO 2016-11-10 21:40:05 MarkDuplicates After output close freeMemory: 8423756128; totalMemory: 8504999936; maxMemory: 11453595648 [Thu Nov 10 21:40:08 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.67 minutes. Runtime.totalMemory()=8504999936 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370892_1/out/align/rep1/SRR1370892_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21849 (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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 36481 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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|
|
|
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.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-------------------- 28211 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370892_1/out/align/rep1/SRR1370892_1.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/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr2/SRR1370892_1.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/pseudo_reps/rep1/pr1/SRR1370892_1.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-------------------- 28210 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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 ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
39220 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/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/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/align/rep1/SRR1370892_1.nodup.15M.tagAlign.gz
opened /tmp/7728.1.q/Rtmp9N8XWq/SRR1370892_1.nodup.15M.tagAlign99761bb687d7
done. read 15000000 fragments
ChIP data read length 69
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1742031
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.179812010789203,0.176663264074804,0.175958005584935
Top 3 estimates for fragment length 155,280,335
Window half size 320
Phantom peak location 70
Phantom peak Correlation 0.1778202
Normalized Strand cross-correlation coefficient (NSC) 1.032198
Relative Strand cross-correlation Coefficient (RSC) 1.550669
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3
| ||||||||||||||||||||||||||||||||||||||||
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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 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/report/SRR1370892_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/report/SRR1370892_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/report/SRR1370892_1_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 3289 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 325
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# 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/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out/qc/rep1/SRR1370892_1.nodup.15M.cc.plot.pdf
--------------------Stdout-------------------- 3316 (process ID) old priority 0, new priority 10 |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6 |
| bool | allowEmpty | false |
| string[] | args | [-title, SRR1370892_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370892_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370892_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| string | ASCPKEY | /software/ascp/etc/asperaweb_id_dsa.openssh |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DERBY_HOME | /usr/lib/jvm/java-8-oracle/db |
| string | DISPLAY | localhost:12.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| string | J2REDIR | /usr/lib/jvm/java-8-oracle/jre |
| string | J2SDKDIR | /usr/lib/jvm/java-8-oracle |
| string | JAVA_HOME | /usr/lib/jvm/java-8-oracle |
| int | K | 1024 |
| string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_N5SeQf |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6 |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESAPPSDIR | /software |
| 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 | /software/ascp/:/software/sratoolkit/2.5.2/bin/:/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/SRR1370892_1 |
| 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/SRR1370892_1 |
| 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 55144 22 |
| string | SSH_CONNECTION | 171.65.77.8 55144 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/4 |
| string | STY | 30759.SRR1370892_1.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 | 20 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |