| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_170957_085 |
| Start time | 2016-11-10 17:09:57 |
| Run time | 12:22:50.594 |
| Tasks executed | 14 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-title, SRR1370882_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370882_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20161110_170957_085/task.graphviz.report.line_97.id_22 chipseq.bds.20161110_170957_085/task.report.pdf2png.line_324.id_27 |
| thread_41 | thread_Root | chipseq.bds.20161110_170957_085_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_13 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_14 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_17 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_18 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_19 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bed.spr_rep1.line_255.id_20 chipseq.bds.20161110_170957_085_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_21 |
| thread_42 | thread_Root | chipseq.bds.20161110_170957_085_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10 chipseq.bds.20161110_170957_085_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161110_170957_085_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20161110_170957_085_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 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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-------------------- 14003 (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/SRR1370882_1/out/align/rep1/SRR1370882_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370882_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.bam
# SYS command. line 149
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_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-------------------- 32505 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.58 sec [bwa_aln_core] refine gapped alignments... 0.71 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 0.67 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.41 sec [bwa_aln_core] refine gapped alignments... 0.64 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.69 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.66 sec [bwa_aln_core] refine gapped alignments... 0.65 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.05 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.28 sec [bwa_aln_core] refine gapped alignments... 0.71 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.04 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.63 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.01 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.35 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.95 sec [bwa_aln_core] refine gapped alignments... 4.89 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.26 sec [bwa_aln_core] refine gapped alignments... 5.15 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.05 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.97 sec [bwa_aln_core] refine gapped alignments... 5.26 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.00 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.15 sec [bwa_aln_core] refine gapped alignments... 3.96 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.29 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.49 sec [bwa_aln_core] refine gapped alignments... 2.46 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.41 sec [bwa_aln_core] refine gapped alignments... 2.25 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.92 sec [bwa_aln_core] refine gapped alignments... 1.23 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.37 sec [bwa_aln_core] refine gapped alignments... 4.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.27 sec [bwa_aln_core] refine gapped alignments... 2.81 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.98 sec [bwa_aln_core] refine gapped alignments... 3.36 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.27 sec [bwa_aln_core] refine gapped alignments... 2.16 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.06 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.54 sec [bwa_aln_core] refine gapped alignments... 3.61 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.51 sec [bwa_aln_core] refine gapped alignments... 3.05 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.19 sec [bwa_aln_core] refine gapped alignments... 3.32 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.37 sec [bwa_aln_core] refine gapped alignments... 3.77 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.21 sec [bwa_aln_core] refine gapped alignments... 3.62 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.72 sec [bwa_aln_core] refine gapped alignments... 4.08 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.76 sec [bwa_aln_core] refine gapped alignments... 7.73 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.98 sec [bwa_aln_core] refine gapped alignments... 6.75 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.74 sec [bwa_aln_core] refine gapped alignments... 11.12 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.59 sec [bwa_aln_core] refine gapped alignments... 9.63 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.47 sec [bwa_aln_core] refine gapped alignments... 5.04 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.17 sec [bwa_aln_core] refine gapped alignments... 7.63 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.59 sec [bwa_aln_core] refine gapped alignments... 5.19 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.82 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.10 sec [bwa_aln_core] refine gapped alignments... 3.97 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.22 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.43 sec [bwa_aln_core] refine gapped alignments... 2.95 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.77 sec [bwa_aln_core] refine gapped alignments... 3.42 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.76 sec [bwa_aln_core] refine gapped alignments... 4.70 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.82 sec [bwa_aln_core] refine gapped alignments... 5.04 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.53 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.42 sec [bwa_aln_core] refine gapped alignments... 4.78 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.53 sec [bwa_aln_core] refine gapped alignments... 1.58 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.31 sec [bwa_aln_core] refine gapped alignments... 4.93 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.37 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 5.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.34 sec [bwa_aln_core] refine gapped alignments... 5.37 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 5.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.83 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.64 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.98 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 5.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.01 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 7.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 20.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.89 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.29 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.24 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 5.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.76 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 7.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.45 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 8.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.10 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 29.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.58 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.95 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.30 sec [bwa_aln_core] refine gapped alignments... 0.63 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 2.11 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.62 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.73 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.25 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.47 sec [bwa_aln_core] refine gapped alignments... 0.64 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.42 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.66 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 5.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 5.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.76 sec [bwa_aln_core] refine gapped alignments... 0.93 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 8.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.21 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 5.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.52 sec [bwa_aln_core] refine gapped alignments... 0.65 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.81 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.38 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.30 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.36 sec [bwa_aln_core] refine gapped alignments... 1.03 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 4.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.34 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.24 sec [bwa_aln_core] refine gapped alignments... 0.64 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.51 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.66 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 5.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.26 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 5.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 6.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.93 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 7.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.90 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 8.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.89 sec [bwa_aln_core] refine gapped alignments... 1.47 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 8.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.94 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.38 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.94 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.32 sec [bwa_aln_core] refine gapped alignments... 4.71 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.27 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.26 sec [bwa_aln_core] refine gapped alignments... 3.79 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.62 sec [bwa_aln_core] refine gapped alignments... 4.13 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.42 sec [bwa_aln_core] refine gapped alignments... 4.00 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.01 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.00 sec [bwa_aln_core] refine gapped alignments... 4.04 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.41 sec [bwa_aln_core] refine gapped alignments... 4.04 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.31 sec [bwa_aln_core] refine gapped alignments... 5.17 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.19 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.31 sec [bwa_aln_core] refine gapped alignments... 4.15 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.89 sec [bwa_aln_core] refine gapped alignments... 4.88 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.15 sec [bwa_aln_core] refine gapped alignments... 8.55 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.82 sec [bwa_aln_core] refine gapped alignments... 4.20 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.41 sec [bwa_aln_core] refine gapped alignments... 8.38 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.82 sec [bwa_aln_core] refine gapped alignments... 3.71 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.73 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.49 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.61 sec [bwa_aln_core] refine gapped alignments... 0.68 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.27 sec [bwa_aln_core] refine gapped alignments... 0.68 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.66 sec [bwa_aln_core] refine gapped alignments... 3.27 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.99 sec [bwa_aln_core] refine gapped alignments... 1.04 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.11 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.22 sec [bwa_aln_core] refine gapped alignments... 0.65 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.87 sec [bwa_aln_core] refine gapped alignments... 1.92 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.82 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.89 sec [bwa_aln_core] refine gapped alignments... 3.98 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.08 sec [bwa_aln_core] refine gapped alignments... 1.95 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.61 sec [bwa_aln_core] refine gapped alignments... 0.69 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.08 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.89 sec [bwa_aln_core] refine gapped alignments... 1.06 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.94 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.20 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.21 sec [bwa_aln_core] refine gapped alignments... 1.18 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.94 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.85 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.99 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.82 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.69 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.93 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.28 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.37 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.31 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 5.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 6.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.97 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 5.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.33 sec [bwa_aln_core] refine gapped alignments... 0.98 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.24 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.20 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.49 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 7.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.24 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 8.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.93 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 7.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.91 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.44 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 5.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 5.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 5.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.56 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 6.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.92 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.90 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.38 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 4.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.20 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.97 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.31 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.66 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.19 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.04 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 6.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.22 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 7.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.45 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 10.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.88 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 7.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.60 sec [bwa_aln_core] refine gapped alignments... 0.63 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.44 sec [bwa_aln_core] refine gapped alignments... 0.71 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.45 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.42 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.49 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.02 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 4.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.18 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 4.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.09 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 4.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.15 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.46 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.20 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.01 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.35 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 7.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.57 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 9.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.33 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 54432638 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/SRR1370882_1/out/align/rep1/SRR1370882_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370882_1.fastq.gz [main] Real time: 3287.427 sec; CPU: 3070.316 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/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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-------------------- 48065 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 19:55:40 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Nov 10 19:55:40 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 19:55:40 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 19:55:40 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 19:55:40 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 19:55:51 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 10s. Last read position: chr1:22,298,551 INFO 2016-11-10 19:55:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:56:00 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 9s. Last read position: chr1:41,895,424 INFO 2016-11-10 19:56:00 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 19:56:08 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 8s. Last read position: chr1:63,396,527 INFO 2016-11-10 19:56:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:56:14 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 5s. Last read position: chr1:89,147,707 INFO 2016-11-10 19:56:14 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:56:20 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: chr1:115,615,553 INFO 2016-11-10 19:56:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:56:29 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 8s. Last read position: chr1:164,468,682 INFO 2016-11-10 19:56:29 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 19:56:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 8s. Last read position: chr1:189,102,252 INFO 2016-11-10 19:56:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:56:43 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 5s. Last read position: chr1:213,979,760 INFO 2016-11-10 19:56:43 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:56:47 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 4s. Last read position: chr1:231,814,268 INFO 2016-11-10 19:56:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:56:56 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 8s. Last read position: chr2:3,652,468 INFO 2016-11-10 19:56:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:57:03 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 7s. Last read position: chr2:39,505,122 INFO 2016-11-10 19:57:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:57:10 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 7s. Last read position: chr2:73,561,393 INFO 2016-11-10 19:57:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:57:14 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 4s. Last read position: chr2:120,526,571 INFO 2016-11-10 19:57:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:57:23 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 8s. Last read position: chr2:160,316,783 INFO 2016-11-10 19:57:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:57:29 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 6s. Last read position: chr2:195,549,735 INFO 2016-11-10 19:57:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:57:36 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 6s. Last read position: chr2:230,358,034 INFO 2016-11-10 19:57:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:57:42 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 6s. Last read position: chr3:16,305,780 INFO 2016-11-10 19:57:42 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 19:57:52 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 9s. Last read position: chr3:49,251,279 INFO 2016-11-10 19:57:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:00 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 8s. Last read position: chr3:84,621,225 INFO 2016-11-10 19:58:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:05 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 4s. Last read position: chr3:128,121,129 INFO 2016-11-10 19:58:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:09 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 4s. Last read position: chr3:165,373,238 INFO 2016-11-10 19:58:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:15 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 6s. Last read position: chr3:195,333,247 INFO 2016-11-10 19:58:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:34 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 18s. Last read position: chr4:37,752,582 INFO 2016-11-10 19:58:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:41 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 6s. Last read position: chr4:81,286,306 INFO 2016-11-10 19:58:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:45 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 4s. Last read position: chr4:119,339,736 INFO 2016-11-10 19:58:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:50 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 5s. Last read position: chr4:158,818,783 INFO 2016-11-10 19:58:50 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 19:59:03 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 13s. Last read position: chr5:6,447,551 INFO 2016-11-10 19:59:03 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-10 19:59:08 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 5s. Last read position: chr5:33,219,021 INFO 2016-11-10 19:59:08 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 19:59:19 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 10s. Last read position: chr5:60,694,078 INFO 2016-11-10 19:59:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:59:24 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 5s. Last read position: chr5:86,336,676 INFO 2016-11-10 19:59:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:31 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 6s. Last read position: chr5:112,930,184 INFO 2016-11-10 19:59:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:59:39 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 8s. Last read position: chr5:136,852,889 INFO 2016-11-10 19:59:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:48 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 8s. Last read position: chr5:160,271,193 INFO 2016-11-10 19:59:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:00 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 11s. Last read position: chr6:4,126,386 INFO 2016-11-10 20:00:00 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:00:04 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 4s. Last read position: chr6:28,666,579 INFO 2016-11-10 20:00:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:00:08 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 4s. Last read position: chr6:49,527,281 INFO 2016-11-10 20:00:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:14 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 5s. Last read position: chr6:81,728,195 INFO 2016-11-10 20:00:14 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:00:22 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 8s. Last read position: chr6:107,535,760 INFO 2016-11-10 20:00:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:00:27 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 4s. Last read position: chr6:132,364,408 INFO 2016-11-10 20:00:27 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:00:31 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 3s. Last read position: chr6:156,918,595 INFO 2016-11-10 20:00:31 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:00:43 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 12s. Last read position: chr7:18,636,743 INFO 2016-11-10 20:00:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:48 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 4s. Last read position: chr7:53,850,313 INFO 2016-11-10 20:00:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 8s. Last read position: chr7:96,503,433 INFO 2016-11-10 20:00:57 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:01:06 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 9s. Last read position: chr7:120,651,846 INFO 2016-11-10 20:01:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:01:52 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 46s. Last read position: chr7:146,401,497 INFO 2016-11-10 20:01:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:00 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 8s. Last read position: chr8:17,030,519 INFO 2016-11-10 20:02:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:09 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 8s. Last read position: chr8:42,750,671 INFO 2016-11-10 20:02:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:13 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 4s. Last read position: chr8:85,385,487 INFO 2016-11-10 20:02:13 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:22 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 8s. Last read position: chr8:124,358,985 INFO 2016-11-10 20:02:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:02:27 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 5s. Last read position: chr9:18,183,883 INFO 2016-11-10 20:02:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:02:39 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 11s. Last read position: chr9:84,163,983 INFO 2016-11-10 20:02:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:02:43 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 4s. Last read position: chr9:119,875,535 INFO 2016-11-10 20:02:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:47 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 3s. Last read position: chr10:5,661,683 INFO 2016-11-10 20:02:47 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:02:52 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 4s. Last read position: chr10:29,748,948 INFO 2016-11-10 20:02:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:03:01 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 8s. Last read position: chr10:61,280,221 INFO 2016-11-10 20:03:01 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:06 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 5s. Last read position: chr10:85,305,552 INFO 2016-11-10 20:03:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:03:12 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 6s. Last read position: chr10:108,129,202 INFO 2016-11-10 20:03:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:16 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 4s. Last read position: chr10:132,730,123 INFO 2016-11-10 20:03:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:03:22 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 5s. Last read position: chr11:35,359,267 INFO 2016-11-10 20:03:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:35 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 13s. Last read position: chr11:75,696,431 INFO 2016-11-10 20:03:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:03:42 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 6s. Last read position: chr11:114,414,621 INFO 2016-11-10 20:03:42 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:03:46 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 4s. Last read position: chr12:8,900,276 INFO 2016-11-10 20:03:46 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:03:51 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 4s. Last read position: chr12:38,863,889 INFO 2016-11-10 20:03:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:55 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 4s. Last read position: chr12:60,598,824 INFO 2016-11-10 20:03:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:00 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 4s. Last read position: chr12:88,520,538 INFO 2016-11-10 20:04:00 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:04:06 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 5s. Last read position: chr12:112,268,437 INFO 2016-11-10 20:04:06 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:19 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 13s. Last read position: chr13:23,999,632 INFO 2016-11-10 20:04:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:24 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 4s. Last read position: chr13:51,165,870 INFO 2016-11-10 20:04:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:04:29 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 5s. Last read position: chr13:88,986,369 INFO 2016-11-10 20:04:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:04:35 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 5s. Last read position: chr14:23,149,367 INFO 2016-11-10 20:04:35 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:04:40 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 5s. Last read position: chr14:58,140,905 INFO 2016-11-10 20:04:40 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:04:45 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 5s. Last read position: chr14:91,912,553 INFO 2016-11-10 20:04:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:04:51 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 5s. Last read position: chr15:38,895,095 INFO 2016-11-10 20:04:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:20 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 29s. Last read position: chr15:68,188,367 INFO 2016-11-10 20:05:20 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:05:25 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 5s. Last read position: chr15:87,921,272 INFO 2016-11-10 20:05:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:32 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 6s. Last read position: chr16:11,143,813 INFO 2016-11-10 20:05:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:46 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 14s. Last read position: chr16:51,391,437 INFO 2016-11-10 20:05:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:05:51 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 5s. Last read position: chr16:84,928,458 INFO 2016-11-10 20:05:51 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:05:59 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 7s. Last read position: chr17:18,368,935 INFO 2016-11-10 20:05:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:05 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 5s. Last read position: chr17:44,246,522 INFO 2016-11-10 20:06:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:10 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 5s. Last read position: chr17:66,172,158 INFO 2016-11-10 20:06:10 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 20:06:15 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 5s. Last read position: chr18:5,619,614 INFO 2016-11-10 20:06:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:21 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 5s. Last read position: chr18:46,152,631 INFO 2016-11-10 20:06:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:26 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 5s. Last read position: chr19:1,328,731 INFO 2016-11-10 20:06:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:32 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 5s. Last read position: chr19:28,148,444 INFO 2016-11-10 20:06:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:48 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 16s. Last read position: chr19:40,341,579 INFO 2016-11-10 20:06:48 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:06:53 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 4s. Last read position: chr20:3,222,035 INFO 2016-11-10 20:06:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:59 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 5s. Last read position: chr20:37,218,903 INFO 2016-11-10 20:06:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:07:35 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 36s. Last read position: chr20:62,871,367 INFO 2016-11-10 20:07:35 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 20:07:40 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 4s. Last read position: chr21:39,474,524 INFO 2016-11-10 20:07:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:07:45 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 5s. Last read position: chr22:31,346,944 INFO 2016-11-10 20:07:45 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:07:50 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 5s. Last read position: chrX:6,235,951 INFO 2016-11-10 20:07:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:07:54 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 4s. Last read position: chrX:38,820,975 INFO 2016-11-10 20:07:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:08:00 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 5s. Last read position: chrX:69,473,954 INFO 2016-11-10 20:08:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:08:06 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 6s. Last read position: chrX:92,683,143 INFO 2016-11-10 20:08:06 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:08:11 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 5s. Last read position: chrX:118,447,518 INFO 2016-11-10 20:08:11 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:08:15 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 3s. Last read position: chrX:142,819,613 INFO 2016-11-10 20:08:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:08:23 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 8s. Last read position: chrM:3,995 INFO 2016-11-10 20:08:23 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-10 20:08:28 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 4s. Last read position: chrM:11,775 INFO 2016-11-10 20:08:28 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-10 20:08:32 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-10 20:08:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 6243635344; totalMemory: 6323437568; maxMemory: 11453595648 INFO 2016-11-10 20:08:38 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 20:08:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 20:08:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 20:09:24 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 20:09:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 6239053704; totalMemory: 9180282880; maxMemory: 11453595648 INFO 2016-11-10 20:09:25 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-10 20:09:25 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-10 20:12:14 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 158s. Last read position: chr2:3,652,468 INFO 2016-11-10 20:18:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:08:43s. Time for last 10,000,000: 365s. Last read position: chr3:128,121,129 INFO 2016-11-10 20:26:52 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:17:17s. Time for last 10,000,000: 513s. Last read position: chr5:86,336,676 INFO 2016-11-10 20:38:32 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:28:57s. Time for last 10,000,000: 699s. Last read position: chr6:156,918,595 INFO 2016-11-10 20:52:14 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:42:38s. Time for last 10,000,000: 821s. Last read position: chr9:18,183,883 INFO 2016-11-10 21:00:16 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:50:40s. Time for last 10,000,000: 481s. Last read position: chr11:75,696,431 INFO 2016-11-10 21:08:30 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:58:55s. Time for last 10,000,000: 494s. Last read position: chr14:23,149,367 INFO 2016-11-10 21:21:55 MarkDuplicates Written 80,000,000 records. Elapsed time: 01:12:19s. Time for last 10,000,000: 804s. Last read position: chr17:44,246,522 INFO 2016-11-10 21:27:42 MarkDuplicates Written 90,000,000 records. Elapsed time: 01:18:06s. Time for last 10,000,000: 347s. Last read position: chr21:39,474,524 INFO 2016-11-10 21:38:20 MarkDuplicates Before output close freeMemory: 9142288480; totalMemory: 9226944512; maxMemory: 11453595648 INFO 2016-11-10 21:39:19 MarkDuplicates After output close freeMemory: 9142811712; totalMemory: 9227468800; maxMemory: 11453595648 [Thu Nov 10 21:39:29 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 103.82 minutes. Runtime.totalMemory()=9227468800 | ||||||||||||||||||||||||||||||||||||||||
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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 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.bam | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 38228 (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/SRR1370882_1/out/align/rep1/SRR1370882_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_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-------------------- 23004 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 20:16:44 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Nov 10 20:16:44 PST 2016] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 20:18:35 MarkDuplicates Start of doWork freeMemory: 254877880; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 20:18:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 20:18:35 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 20:21:59 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 159s. Last read position: chr1:51,971,134 INFO 2016-11-10 20:21:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:23:03 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 64s. Last read position: chr1:99,847,528 INFO 2016-11-10 20:23:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:24:10 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 66s. Last read position: chr1:177,810,655 INFO 2016-11-10 20:24:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:25:38 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 87s. Last read position: chr1:226,123,896 INFO 2016-11-10 20:25:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:26:46 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 68s. Last read position: chr2:30,623,099 INFO 2016-11-10 20:26:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:27:44 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 57s. Last read position: chr2:113,030,429 INFO 2016-11-10 20:27:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:28:53 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 69s. Last read position: chr2:184,242,788 INFO 2016-11-10 20:28:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:31:45 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 171s. Last read position: chr3:11,664,252 INFO 2016-11-10 20:31:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:33:10 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 85s. Last read position: chr3:77,087,933 INFO 2016-11-10 20:33:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:34:01 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 51s. Last read position: chr3:156,690,831 INFO 2016-11-10 20:34:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:37:11 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:17:50s. Time for last 1,000,000: 189s. Last read position: chr4:33,881,342 INFO 2016-11-10 20:37:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:38:35 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 84s. Last read position: chr4:111,071,505 INFO 2016-11-10 20:38:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:42:14 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:22:54s. Time for last 1,000,000: 218s. Last read position: chr4:188,208,891 INFO 2016-11-10 20:42:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:45:00 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:25:39s. Time for last 1,000,000: 165s. Last read position: chr5:58,859,264 INFO 2016-11-10 20:45:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:46:02 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:26:41s. Time for last 1,000,000: 62s. Last read position: chr5:107,286,445 INFO 2016-11-10 20:46:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:47:39 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:28:19s. Time for last 1,000,000: 97s. Last read position: chr5:154,174,014 INFO 2016-11-10 20:47:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:51:13 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:31:52s. Time for last 1,000,000: 213s. Last read position: chr6:22,895,263 INFO 2016-11-10 20:51:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:57:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:38:16s. Time for last 1,000,000: 383s. Last read position: chr6:82,596,290 INFO 2016-11-10 20:57:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:01:00 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:41:39s. Time for last 1,000,000: 203s. Last read position: chr6:130,557,933 INFO 2016-11-10 21:01:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:02:01 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:42:40s. Time for last 1,000,000: 61s. Last read position: chr7:14,186,085 INFO 2016-11-10 21:02:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:07:25 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:48:05s. Time for last 1,000,000: 324s. Last read position: chr7:92,736,418 INFO 2016-11-10 21:07:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:09:59 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:50:38s. Time for last 1,000,000: 153s. Last read position: chr7:143,445,433 INFO 2016-11-10 21:09:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:11:09 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:51:48s. Time for last 1,000,000: 69s. Last read position: chr8:51,718,783 INFO 2016-11-10 21:11:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:16:23 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:57:03s. Time for last 1,000,000: 314s. Last read position: chr8:127,643,532 INFO 2016-11-10 21:16:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:21:31 MarkDuplicates Read 25,000,000 records. Elapsed time: 01:02:11s. Time for last 1,000,000: 308s. Last read position: chr9:87,025,601 INFO 2016-11-10 21:21:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:22:35 MarkDuplicates Read 26,000,000 records. Elapsed time: 01:03:14s. Time for last 1,000,000: 63s. Last read position: chr10:13,128,234 INFO 2016-11-10 21:22:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:25:39 MarkDuplicates Read 27,000,000 records. Elapsed time: 01:06:19s. Time for last 1,000,000: 184s. Last read position: chr10:70,880,120 INFO 2016-11-10 21:25:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:28:34 MarkDuplicates Read 28,000,000 records. Elapsed time: 01:09:14s. Time for last 1,000,000: 174s. Last read position: chr10:121,235,164 INFO 2016-11-10 21:28:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:32:21 MarkDuplicates Read 29,000,000 records. Elapsed time: 01:13:01s. Time for last 1,000,000: 227s. Last read position: chr11:67,840,347 INFO 2016-11-10 21:32:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:36:02 MarkDuplicates Read 30,000,000 records. Elapsed time: 01:16:41s. Time for last 1,000,000: 220s. Last read position: chr12:5,834,198 INFO 2016-11-10 21:36:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:37:18 MarkDuplicates Read 31,000,000 records. Elapsed time: 01:17:58s. Time for last 1,000,000: 76s. Last read position: chr12:59,381,935 INFO 2016-11-10 21:37:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:40:00 MarkDuplicates Read 32,000,000 records. Elapsed time: 01:20:39s. Time for last 1,000,000: 161s. Last read position: chr12:111,363,347 INFO 2016-11-10 21:40:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:41:07 MarkDuplicates Read 33,000,000 records. Elapsed time: 01:21:46s. Time for last 1,000,000: 66s. Last read position: chr13:51,862,023 INFO 2016-11-10 21:41:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:44:10 MarkDuplicates Read 34,000,000 records. Elapsed time: 01:24:49s. Time for last 1,000,000: 182s. Last read position: chr13:113,183,261 INFO 2016-11-10 21:44:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 21:57:25 MarkDuplicates Read 35,000,000 records. Elapsed time: 01:38:04s. Time for last 1,000,000: 794s. Last read position: chr14:87,314,938 INFO 2016-11-10 21:57:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:04:31 MarkDuplicates Read 36,000,000 records. Elapsed time: 01:45:10s. Time for last 1,000,000: 426s. Last read position: chr15:72,018,377 INFO 2016-11-10 22:04:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:15:23 MarkDuplicates Read 37,000,000 records. Elapsed time: 01:56:03s. Time for last 1,000,000: 652s. Last read position: chr16:48,096,815 INFO 2016-11-10 22:15:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:15:57 MarkDuplicates Read 38,000,000 records. Elapsed time: 01:56:36s. Time for last 1,000,000: 33s. Last read position: chr17:32,928,603 INFO 2016-11-10 22:15:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:23:28 MarkDuplicates Read 39,000,000 records. Elapsed time: 02:04:08s. Time for last 1,000,000: 451s. Last read position: chr18:8,487,793 INFO 2016-11-10 22:23:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:33:01 MarkDuplicates Read 40,000,000 records. Elapsed time: 02:13:41s. Time for last 1,000,000: 572s. Last read position: chr19:11,853,750 INFO 2016-11-10 22:33:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:36:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 02:16:41s. Time for last 1,000,000: 179s. Last read position: chr20:11,656,371 INFO 2016-11-10 22:36:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:43:39 MarkDuplicates Read 42,000,000 records. Elapsed time: 02:24:18s. Time for last 1,000,000: 457s. Last read position: chr21:38,741,929 INFO 2016-11-10 22:43:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:50:15 MarkDuplicates Read 43,000,000 records. Elapsed time: 02:30:54s. Time for last 1,000,000: 395s. Last read position: chrX:21,950,752 INFO 2016-11-10 22:50:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 22:51:04 MarkDuplicates Read 44,000,000 records. Elapsed time: 02:31:43s. Time for last 1,000,000: 48s. Last read position: chrX:82,319,806 INFO 2016-11-10 22:51:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:11:34 MarkDuplicates Read 45,000,000 records. Elapsed time: 02:52:14s. Time for last 1,000,000: 1,230s. Last read position: chrX:140,499,104 INFO 2016-11-10 23:11:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 23:12:57 MarkDuplicates Read 45340893 records. 0 pairs never matched. INFO 2016-11-10 23:15:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 7218894984; totalMemory: 7474774016; maxMemory: 11453595648 INFO 2016-11-10 23:15:56 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 23:16:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 23:16:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 23:20:52 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 23:20:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 5886198976; totalMemory: 8828485632; maxMemory: 11453595648 INFO 2016-11-10 23:20:55 MarkDuplicates Marking 14085784 records as duplicates. INFO 2016-11-10 23:20:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-11 01:31:53 MarkDuplicates Written 10,000,000 records. Elapsed time: 02:10:03s. Time for last 10,000,000: 7,803s. Last read position: chr3:156,690,831 INFO 2016-11-11 02:33:25 MarkDuplicates Written 20,000,000 records. Elapsed time: 03:11:34s. Time for last 10,000,000: 3,691s. Last read position: chr7:14,186,085 INFO 2016-11-11 04:04:03 MarkDuplicates Written 30,000,000 records. Elapsed time: 04:42:12s. Time for last 10,000,000: 5,438s. Last read position: chr12:5,834,198 INFO 2016-11-11 04:48:41 MarkDuplicates Written 40,000,000 records. Elapsed time: 05:26:50s. Time for last 10,000,000: 2,678s. Last read position: chr19:11,853,750 INFO 2016-11-11 05:05:01 MarkDuplicates Before output close freeMemory: 8735606872; totalMemory: 8819572736; maxMemory: 11453595648 INFO 2016-11-11 05:05:49 MarkDuplicates After output close freeMemory: 8782789896; totalMemory: 8866758656; maxMemory: 11453595648 [Fri Nov 11 05:05:50 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 529.11 minutes. Runtime.totalMemory()=8866758656 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 153
sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 155
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_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/SRR1370882_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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 48220 (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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 36920 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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|
# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.bam
# SYS command. line 153
sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 733 (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 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 46520 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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|
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_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-------------------- 46689 (process ID) old priority 0, new priority 10 Waiting for 23 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_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/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr2/SRR1370882_1.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/pseudo_reps/rep1/pr1/SRR1370882_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-------------------- 46688 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 214
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
51025 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 3
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/align/rep1/SRR1370882_1.nodup.15M.tagAlign.gz
opened /tmp/8052.1.q/RtmpEt55WD/SRR1370882_1.nodup.15M.tagAlignc79b3c3d75d3
done. read 15000000 fragments
ChIP data read length 109
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1743272
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.190846576271836,0.177043836183906,0.176827818008163
Top 3 estimates for fragment length 180,495,510
Window half size 400
Phantom peak location 115
Phantom peak Correlation 0.1857943
Normalized Strand cross-correlation coefficient (NSC) 1.09476
Relative Strand cross-correlation Coefficient (RSC) 1.440588
Phantom Peak Quality Tag 1
null device
1
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3
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# SYS command. line 98
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/report/SRR1370882_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/report/SRR1370882_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/report/SRR1370882_1_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 52066 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
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# SYS command. line 325
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 326
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out/qc/rep1/SRR1370882_1.nodup.15M.cc.plot.pdf
--------------------Stdout-------------------- 52102 (process ID) old priority 0, new priority 10 |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6 |
| bool | allowEmpty | false |
| string[] | args | [-title, SRR1370882_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370882_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370882_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/SRR1370882_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/SRR1370882_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 | 29294.SRR1370882_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 |