| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161113_130747_722 |
| Start time | 2016-11-13 13:07:47 |
| Run time | 07:34:06.419 |
| Tasks executed | 12 |
| Tasks failed | 1 |
| Tasks failed names | xcor rep1 |
| Arguments* | [-title, SRR1370880_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370880_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 | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_41 | thread_Root | chipseq.bds.20161113_130747_722_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_13 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_17 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_18 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_19 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bed.spr_rep1.line_255.id_20 chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21 |
| thread_42 | thread_Root | chipseq.bds.20161113_130747_722_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161113_130747_722_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161113_130747_722_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20161113_130747_722_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_16 |
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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/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_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/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_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/SRR1370880_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-------------------- 13948 (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/SRR1370880_1/out/align/rep1/SRR1370880_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370880_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_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-------------------- 8836 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.57 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 0.56 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.60 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.09 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.67 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.76 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.83 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.69 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.68 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.67 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.76 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.34 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.03 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.69 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.65 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.61 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.77 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.70 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.64 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.35 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.05 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.13 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.09 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.00 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.90 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.66 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.22 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.64 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.75 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.58 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.38 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.13 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.13 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.33 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.05 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.79 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.48 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.49 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.07 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.63 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.80 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.99 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.20 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.93 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.63 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.35 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.58 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.88 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.79 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.24 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.08 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.39 sec [bwa_aln_core] refine gapped alignments... 2.72 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.67 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.09 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.27 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.75 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.81 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.74 sec [bwa_aln_core] refine gapped alignments... 1.00 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.07 sec [bwa_aln_core] refine gapped alignments... 1.06 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.39 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.01 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.39 sec [bwa_aln_core] refine gapped alignments... 1.55 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.78 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.54 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.94 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.28 sec [bwa_aln_core] refine gapped alignments... 4.60 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.10 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.53 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.50 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.73 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.57 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.37 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.86 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.01 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.99 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.01 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.26 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.36 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.43 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.68 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.65 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.95 sec [bwa_aln_core] refine gapped alignments... 1.41 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.27 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.93 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.86 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.13 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.07 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.90 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.13 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.82 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.29 sec [bwa_aln_core] refine gapped alignments... 1.18 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.94 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.05 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.55 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.96 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.82 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.99 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.29 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.82 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.86 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.88 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.10 sec [bwa_aln_core] 27304732 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/SRR1370880_1/out/align/rep1/SRR1370880_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370880_1.fastq.gz [main] Real time: 1279.217 sec; CPU: 1110.992 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/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_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/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_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-------------------- 40937 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Sun Nov 13 15:29:19 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_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 [Sun Nov 13 15:29:19 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-13 15:29:20 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-13 15:29:20 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-13 15:29:20 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-13 15:29:28 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:22,298,551 INFO 2016-11-13 15:29:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:29:35 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 7s. Last read position: chr1:41,895,424 INFO 2016-11-13 15:29:35 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:29:41 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 5s. Last read position: chr1:63,396,527 INFO 2016-11-13 15:29:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:29:48 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 6s. Last read position: chr1:89,147,707 INFO 2016-11-13 15:29:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:29:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 5s. Last read position: chr1:115,615,553 INFO 2016-11-13 15:29:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:29:58 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 5s. Last read position: chr1:164,468,682 INFO 2016-11-13 15:29:58 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:30:05 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 6s. Last read position: chr1:189,102,252 INFO 2016-11-13 15:30:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:30:11 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 5s. Last read position: chr1:213,979,760 INFO 2016-11-13 15:30:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:30:15 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 4s. Last read position: chr1:231,814,268 INFO 2016-11-13 15:30:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:30:20 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 4s. Last read position: chr2:3,652,468 INFO 2016-11-13 15:30:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:30:27 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 6s. Last read position: chr2:39,505,122 INFO 2016-11-13 15:30:27 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:30:33 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 5s. Last read position: chr2:73,561,393 INFO 2016-11-13 15:30:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:30:37 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 4s. Last read position: chr2:120,526,571 INFO 2016-11-13 15:30:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:30:44 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 6s. Last read position: chr2:160,316,783 INFO 2016-11-13 15:30:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:30:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 5s. Last read position: chr2:195,549,735 INFO 2016-11-13 15:30:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:30:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 7s. Last read position: chr2:230,358,034 INFO 2016-11-13 15:30:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:31:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 4s. Last read position: chr3:16,305,780 INFO 2016-11-13 15:31:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:31:08 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 5s. Last read position: chr3:49,251,279 INFO 2016-11-13 15:31:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:31:13 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 5s. Last read position: chr3:84,621,225 INFO 2016-11-13 15:31:13 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:31:18 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 5s. Last read position: chr3:128,121,129 INFO 2016-11-13 15:31:18 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:31:27 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 8s. Last read position: chr3:165,373,238 INFO 2016-11-13 15:31:27 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:31:32 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 4s. Last read position: chr3:195,333,247 INFO 2016-11-13 15:31:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:31:36 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 4s. Last read position: chr4:37,752,582 INFO 2016-11-13 15:31:36 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:31:41 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 5s. Last read position: chr4:81,286,306 INFO 2016-11-13 15:31:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:31:46 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 5s. Last read position: chr4:119,339,736 INFO 2016-11-13 15:31:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:31:51 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 4s. Last read position: chr4:158,818,783 INFO 2016-11-13 15:31:51 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:31:55 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr5:6,447,551 INFO 2016-11-13 15:31:55 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-13 15:32:04 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 9s. Last read position: chr5:33,219,021 INFO 2016-11-13 15:32:04 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:32:10 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 5s. Last read position: chr5:60,694,078 INFO 2016-11-13 15:32:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:32:14 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 4s. Last read position: chr5:86,336,676 INFO 2016-11-13 15:32:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:32:18 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 4s. Last read position: chr5:112,930,184 INFO 2016-11-13 15:32:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:32:24 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 5s. Last read position: chr5:136,852,889 INFO 2016-11-13 15:32:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:32:50 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 26s. Last read position: chr5:160,271,193 INFO 2016-11-13 15:32:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:33:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 11s. Last read position: chr6:4,126,386 INFO 2016-11-13 15:33:01 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:33:07 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 5s. Last read position: chr6:28,666,579 INFO 2016-11-13 15:33:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:33:12 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 4s. Last read position: chr6:49,527,281 INFO 2016-11-13 15:33:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:33:16 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 4s. Last read position: chr6:81,728,195 INFO 2016-11-13 15:33:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:33:21 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 4s. Last read position: chr6:107,535,760 INFO 2016-11-13 15:33:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:33:25 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 4s. Last read position: chr6:132,364,408 INFO 2016-11-13 15:33:25 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:33:30 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 4s. Last read position: chr6:156,918,595 INFO 2016-11-13 15:33:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:33:35 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 4s. Last read position: chr7:18,636,743 INFO 2016-11-13 15:33:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:33:40 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 5s. Last read position: chr7:53,850,313 INFO 2016-11-13 15:33:40 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:33:54 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 13s. Last read position: chr7:96,503,433 INFO 2016-11-13 15:33:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:33:58 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 4s. Last read position: chr7:120,651,846 INFO 2016-11-13 15:33:58 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:34:45 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 46s. Last read position: chr7:146,401,497 INFO 2016-11-13 15:34:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:34:51 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 5s. Last read position: chr8:17,030,519 INFO 2016-11-13 15:34:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:34:56 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 5s. Last read position: chr8:42,750,671 INFO 2016-11-13 15:34:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:35:02 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 5s. Last read position: chr8:85,385,487 INFO 2016-11-13 15:35:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:35:08 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 5s. Last read position: chr8:124,358,985 INFO 2016-11-13 15:35:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:35:13 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 5s. Last read position: chr9:18,183,883 INFO 2016-11-13 15:35:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:35:18 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 4s. Last read position: chr9:84,163,983 INFO 2016-11-13 15:35:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:35:25 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 6s. Last read position: chr9:119,875,535 INFO 2016-11-13 15:35:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:35:31 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 6s. Last read position: chr10:5,661,683 INFO 2016-11-13 15:35:31 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:35:38 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 6s. Last read position: chr10:29,748,948 INFO 2016-11-13 15:35:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:35:43 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 5s. Last read position: chr10:61,280,221 INFO 2016-11-13 15:35:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:35:48 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 5s. Last read position: chr10:85,305,552 INFO 2016-11-13 15:35:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:35:59 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 10s. Last read position: chr10:108,129,202 INFO 2016-11-13 15:35:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:36:04 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 5s. Last read position: chr10:132,730,123 INFO 2016-11-13 15:36:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:36:10 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 6s. Last read position: chr11:35,359,267 INFO 2016-11-13 15:36:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:36:16 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 5s. Last read position: chr11:75,696,431 INFO 2016-11-13 15:36:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:36:22 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 6s. Last read position: chr11:114,414,621 INFO 2016-11-13 15:36:22 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:36:27 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 5s. Last read position: chr12:8,900,276 INFO 2016-11-13 15:36:27 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:36:34 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 6s. Last read position: chr12:38,863,889 INFO 2016-11-13 15:36:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:36:39 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 5s. Last read position: chr12:60,598,824 INFO 2016-11-13 15:36:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:36:44 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 4s. Last read position: chr12:88,520,538 INFO 2016-11-13 15:36:44 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:36:49 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 5s. Last read position: chr12:112,268,437 INFO 2016-11-13 15:36:49 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:37:00 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 11s. Last read position: chr13:23,999,632 INFO 2016-11-13 15:37:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:37:07 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 6s. Last read position: chr13:51,165,870 INFO 2016-11-13 15:37:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:37:13 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 6s. Last read position: chr13:88,986,369 INFO 2016-11-13 15:37:13 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:18 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 4s. Last read position: chr14:23,149,367 INFO 2016-11-13 15:37:18 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:37:24 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 6s. Last read position: chr14:58,140,905 INFO 2016-11-13 15:37:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:29 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 5s. Last read position: chr14:91,912,553 INFO 2016-11-13 15:37:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:37:34 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr15:38,895,095 INFO 2016-11-13 15:37:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:39 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 4s. Last read position: chr15:68,188,367 INFO 2016-11-13 15:37:39 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:37:44 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 5s. Last read position: chr15:87,921,272 INFO 2016-11-13 15:37:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:50 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 5s. Last read position: chr16:11,143,813 INFO 2016-11-13 15:37:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:37:56 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 5s. Last read position: chr16:51,391,437 INFO 2016-11-13 15:37:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:38:08 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 12s. Last read position: chr16:84,928,458 INFO 2016-11-13 15:38:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:15 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 6s. Last read position: chr17:18,368,935 INFO 2016-11-13 15:38:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:21 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 5s. Last read position: chr17:44,246,522 INFO 2016-11-13 15:38:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:26 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 5s. Last read position: chr17:66,172,158 INFO 2016-11-13 15:38:26 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-13 15:38:33 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 6s. Last read position: chr18:5,619,614 INFO 2016-11-13 15:38:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:39 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 5s. Last read position: chr18:46,152,631 INFO 2016-11-13 15:38:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:45 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 6s. Last read position: chr19:1,328,731 INFO 2016-11-13 15:38:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:38:52 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 6s. Last read position: chr19:28,148,444 INFO 2016-11-13 15:38:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:38:58 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 5s. Last read position: chr19:40,341,579 INFO 2016-11-13 15:38:58 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:39:03 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 5s. Last read position: chr20:3,222,035 INFO 2016-11-13 15:39:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:39:09 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 6s. Last read position: chr20:37,218,903 INFO 2016-11-13 15:39:09 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:01 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 51s. Last read position: chr20:62,871,367 INFO 2016-11-13 15:40:01 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-13 15:40:07 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 6s. Last read position: chr21:39,474,524 INFO 2016-11-13 15:40:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:14 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 6s. Last read position: chr22:31,346,944 INFO 2016-11-13 15:40:14 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-13 15:40:21 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 7s. Last read position: chrX:6,235,951 INFO 2016-11-13 15:40:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:40:29 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 7s. Last read position: chrX:38,820,975 INFO 2016-11-13 15:40:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-13 15:40:35 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 5s. Last read position: chrX:69,473,954 INFO 2016-11-13 15:40:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:41 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 6s. Last read position: chrX:92,683,143 INFO 2016-11-13 15:40:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-13 15:40:48 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 6s. Last read position: chrX:118,447,518 INFO 2016-11-13 15:40:48 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-13 15:40:56 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 7s. Last read position: chrX:142,819,613 INFO 2016-11-13 15:40:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:41:06 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 10s. Last read position: chrM:3,995 INFO 2016-11-13 15:41:06 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-13 15:41:11 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 5s. Last read position: chrM:11,775 INFO 2016-11-13 15:41:11 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-13 15:41:17 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-13 15:41:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 5755465024; totalMemory: 5804916736; maxMemory: 11453595648 INFO 2016-11-13 15:41:29 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-13 15:41:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-13 15:41:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-13 15:42:05 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-13 15:42:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 5039063328; totalMemory: 7956070400; maxMemory: 11453595648 INFO 2016-11-13 15:42:05 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-13 15:42:05 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-13 15:44:19 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:13s. Time for last 10,000,000: 133s. Last read position: chr2:3,652,468 INFO 2016-11-13 15:46:49 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 149s. Last read position: chr3:128,121,129 INFO 2016-11-13 15:49:36 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:07:30s. Time for last 10,000,000: 167s. Last read position: chr5:86,336,676 INFO 2016-11-13 15:52:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:10:07s. Time for last 10,000,000: 157s. Last read position: chr6:156,918,595 INFO 2016-11-13 15:54:59 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:12:53s. Time for last 10,000,000: 165s. Last read position: chr9:18,183,883 INFO 2016-11-13 15:57:39 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:15:33s. Time for last 10,000,000: 160s. Last read position: chr11:75,696,431 INFO 2016-11-13 16:00:24 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:18:18s. Time for last 10,000,000: 164s. Last read position: chr14:23,149,367 INFO 2016-11-13 16:03:33 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:21:27s. Time for last 10,000,000: 189s. Last read position: chr17:44,246,522 INFO 2016-11-13 16:06:38 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:24:33s. Time for last 10,000,000: 185s. Last read position: chr21:39,474,524 INFO 2016-11-13 16:09:21 MarkDuplicates Before output close freeMemory: 8549674376; totalMemory: 8617197568; maxMemory: 11453595648 INFO 2016-11-13 16:09:21 MarkDuplicates After output close freeMemory: 8553269944; totalMemory: 8620867584; maxMemory: 11453595648 [Sun Nov 13 16:09:21 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 40.03 minutes. Runtime.totalMemory()=8620867584 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370880_1/out/align/rep1/SRR1370880_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 1863 (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/SRR1370880_1/out/align/rep1/SRR1370880_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_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-------------------- 22316 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Sun Nov 13 18:23:40 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_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 [Sun Nov 13 18:23:40 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-13 18:23:41 MarkDuplicates Start of doWork freeMemory: 254879488; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-13 18:23:41 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-13 18:23:41 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-13 18:23:51 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr1:97,218,681 INFO 2016-11-13 18:23:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:00 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 9s. Last read position: chr1:228,934,514 INFO 2016-11-13 18:24:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:09 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 8s. Last read position: chr2:137,223,539 INFO 2016-11-13 18:24:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:16 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 6s. Last read position: chr3:46,685,770 INFO 2016-11-13 18:24:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:22 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: chr4:15,226,293 INFO 2016-11-13 18:24:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:25 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: chr5:5,287,328 INFO 2016-11-13 18:24:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:29 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: chr5:120,238,821 INFO 2016-11-13 18:24:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:34 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 5s. Last read position: chr6:43,760,394 INFO 2016-11-13 18:24:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:39 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 5s. Last read position: chr6:159,318,325 INFO 2016-11-13 18:24:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:48 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 8s. Last read position: chr7:136,086,899 INFO 2016-11-13 18:24:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:24:54 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 5s. Last read position: chr8:127,413,724 INFO 2016-11-13 18:24:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:01 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 6s. Last read position: chr10:17,244,715 INFO 2016-11-13 18:25:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:06 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 5s. Last read position: chr10:129,716,697 INFO 2016-11-13 18:25:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:12 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 5s. Last read position: chr12:19,168,868 INFO 2016-11-13 18:25:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:15 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: chr12:130,762,528 INFO 2016-11-13 18:25:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:19 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr14:53,128,730 INFO 2016-11-13 18:25:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:22 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: chr15:98,251,757 INFO 2016-11-13 18:25:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:33 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 10s. Last read position: chr17:48,642,549 INFO 2016-11-13 18:25:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:38 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 4s. Last read position: chr19:18,644,453 INFO 2016-11-13 18:25:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:50 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 12s. Last read position: chr21:26,253,638 INFO 2016-11-13 18:25:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:25:56 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 5s. Last read position: chrX:48,535,893 INFO 2016-11-13 18:25:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 18:26:03 MarkDuplicates Read 21982739 records. 0 pairs never matched. INFO 2016-11-13 18:26:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 4313781376; totalMemory: 6152519680; maxMemory: 11453595648 INFO 2016-11-13 18:26:08 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-13 18:26:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-13 18:26:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-13 18:26:09 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-13 18:26:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 6073636120; totalMemory: 9015656448; maxMemory: 11453595648 INFO 2016-11-13 18:26:45 MarkDuplicates Marking 1204795 records as duplicates. INFO 2016-11-13 18:26:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-13 18:28:11 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 86s. Last read position: chr7:136,086,899 INFO 2016-11-13 18:29:41 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:56s. Time for last 10,000,000: 89s. Last read position: chr21:26,253,638 INFO 2016-11-13 18:29:59 MarkDuplicates Before output close freeMemory: 8827057216; totalMemory: 8909225984; maxMemory: 11453595648 INFO 2016-11-13 18:29:59 MarkDuplicates After output close freeMemory: 8941875128; totalMemory: 9024045056; maxMemory: 11453595648 [Sun Nov 13 18:29:59 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.31 minutes. Runtime.totalMemory()=9024045056 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21865 (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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 25424 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 33375 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# 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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 22785 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_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-------------------- 12303 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# 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/SRR1370880_1/out/align/rep1/SRR1370880_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/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr2/SRR1370880_1.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/pseudo_reps/rep1/pr1/SRR1370880_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-------------------- 32312 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# 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 ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/align/rep1/SRR1370880_1.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out/qc/rep1/SRR1370880_1.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
3412 (process ID) old priority 0, new priority 10
--------------------Post mortem info--------------------
==============================================================
job_number: 9961
exec_file: job_scripts/9961
submission_time: Sun Nov 13 20:41:35 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/SRR1370880_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/chipseq.bds.20161113_130747_722_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21.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=8173.SRR1370880_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/SRR1370880_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
usage 1: cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info: queue instance "q@surya" 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@kadru" dropped because it is full
queue instance "amd.q@wotan" dropped because it is full
|
| 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, SRR1370880_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370880_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370880_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/SRR1370880_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/SRR1370880_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 | 8173.SRR1370880_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 |