| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_171047_124 |
| Start time | 2016-11-10 17:10:47 |
| Run time | 09:29:31.204 |
| Tasks executed | 13 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-title, SRR1370906_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370906_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_171047_124/task.graphviz.report.line_97.id_21 chipseq.bds.20161110_171047_124/task.report.pdf2png.line_324.id_26 |
| thread_41 | thread_Root | chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_10 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_13 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_16 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_17 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_18 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bed.spr_rep1.line_255.id_19 chipseq.bds.20161110_171047_124_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_20 |
| thread_42 | thread_Root | chipseq.bds.20161110_171047_124_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161110_171047_124_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 chipseq.bds.20161110_171047_124_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_14 chipseq.bds.20161110_171047_124_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_15 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_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-------------------- 13221 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 6822 (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/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_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/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_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-------------------- 5641 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 19:55:35 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_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 19:55:35 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-10 19:55:35 MarkDuplicates Start of doWork freeMemory: 254879200; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 19:55:35 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 19:55:35 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 19:55:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:22,298,551 INFO 2016-11-10 19:55:57 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:56:11 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 13s. Last read position: chr1:41,895,424 INFO 2016-11-10 19:56:11 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 19:56:27 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 15s. Last read position: chr1:63,396,527 INFO 2016-11-10 19:56:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:56:36 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 9s. Last read position: chr1:89,147,707 INFO 2016-11-10 19:56:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:56:51 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 14s. Last read position: chr1:115,615,553 INFO 2016-11-10 19:56:51 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:57:05 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 13s. Last read position: chr1:164,468,682 INFO 2016-11-10 19:57:05 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 19:57:16 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 10s. Last read position: chr1:189,102,252 INFO 2016-11-10 19:57:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:57:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 5s. Last read position: chr1:213,979,760 INFO 2016-11-10 19:57:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:57:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 21s. Last read position: chr1:231,814,268 INFO 2016-11-10 19:57:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:57:47 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 4s. Last read position: chr2:3,652,468 INFO 2016-11-10 19:57:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:57:54 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 6s. Last read position: chr2:39,505,122 INFO 2016-11-10 19:57:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:07 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 12s. Last read position: chr2:73,561,393 INFO 2016-11-10 19:58:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:58:11 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 4s. Last read position: chr2:120,526,571 INFO 2016-11-10 19:58:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:58:20 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 8s. Last read position: chr2:160,316,783 INFO 2016-11-10 19:58:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:30 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 10s. Last read position: chr2:195,549,735 INFO 2016-11-10 19:58:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:58:45 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 14s. Last read position: chr2:230,358,034 INFO 2016-11-10 19:58:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 19:58:49 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 4s. Last read position: chr3:16,305,780 INFO 2016-11-10 19:58:49 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 19:58:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 9s. Last read position: chr3:49,251,279 INFO 2016-11-10 19:58:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:08 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 8s. Last read position: chr3:84,621,225 INFO 2016-11-10 19:59:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:59:20 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 12s. Last read position: chr3:128,121,129 INFO 2016-11-10 19:59:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:59:24 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 4s. Last read position: chr3:165,373,238 INFO 2016-11-10 19:59:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:30 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 5s. Last read position: chr3:195,333,247 INFO 2016-11-10 19:59:30 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:38 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 7s. Last read position: chr4:37,752,582 INFO 2016-11-10 19:59:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 19:59:47 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 9s. Last read position: chr4:81,286,306 INFO 2016-11-10 19:59:47 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:59:54 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 7s. Last read position: chr4:119,339,736 INFO 2016-11-10 19:59:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 19:59:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 4s. Last read position: chr4:158,818,783 INFO 2016-11-10 19:59:59 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:00:05 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 6s. Last read position: chr5:6,447,551 INFO 2016-11-10 20:00:05 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-11-10 20:00:19 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 14s. Last read position: chr5:33,219,021 INFO 2016-11-10 20:00:19 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:00:24 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 5s. Last read position: chr5:60,694,078 INFO 2016-11-10 20:00:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:00:29 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 4s. Last read position: chr5:86,336,676 INFO 2016-11-10 20:00:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:38 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 8s. Last read position: chr5:112,930,184 INFO 2016-11-10 20:00:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:00:44 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 5s. Last read position: chr5:136,852,889 INFO 2016-11-10 20:00:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:00:48 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 4s. Last read position: chr5:160,271,193 INFO 2016-11-10 20:00:48 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:01:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 14s. Last read position: chr6:4,126,386 INFO 2016-11-10 20:01:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:01:08 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 5s. Last read position: chr6:28,666,579 INFO 2016-11-10 20:01:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:01:17 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 8s. Last read position: chr6:49,527,281 INFO 2016-11-10 20:01:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:01:22 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 5s. Last read position: chr6:81,728,195 INFO 2016-11-10 20:01:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:01:28 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 5s. Last read position: chr6:107,535,760 INFO 2016-11-10 20:01:28 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:01:41 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 13s. Last read position: chr6:132,364,408 INFO 2016-11-10 20:01:41 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:01:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 9s. Last read position: chr6:156,918,595 INFO 2016-11-10 20:01:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:01:56 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 5s. Last read position: chr7:18,636,743 INFO 2016-11-10 20:01:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:06 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 10s. Last read position: chr7:53,850,313 INFO 2016-11-10 20:02:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:02:15 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 8s. Last read position: chr7:96,503,433 INFO 2016-11-10 20:02:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:02:22 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 7s. Last read position: chr7:120,651,846 INFO 2016-11-10 20:02:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:07 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 44s. Last read position: chr7:146,401,497 INFO 2016-11-10 20:03:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:14 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 7s. Last read position: chr8:17,030,519 INFO 2016-11-10 20:03:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:23 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 9s. Last read position: chr8:42,750,671 INFO 2016-11-10 20:03:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:28 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 4s. Last read position: chr8:85,385,487 INFO 2016-11-10 20:03:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:03:36 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 8s. Last read position: chr8:124,358,985 INFO 2016-11-10 20:03:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:03:43 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 6s. Last read position: chr9:18,183,883 INFO 2016-11-10 20:03:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:03:50 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 6s. Last read position: chr9:84,163,983 INFO 2016-11-10 20:03:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:03:55 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 5s. Last read position: chr9:119,875,535 INFO 2016-11-10 20:03:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:04:00 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 5s. Last read position: chr10:5,661,683 INFO 2016-11-10 20:04:00 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:04:11 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 10s. Last read position: chr10:29,748,948 INFO 2016-11-10 20:04:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:18 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 7s. Last read position: chr10:61,280,221 INFO 2016-11-10 20:04:18 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:04:23 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 5s. Last read position: chr10:85,305,552 INFO 2016-11-10 20:04:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:04:31 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 7s. Last read position: chr10:108,129,202 INFO 2016-11-10 20:04:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:04:38 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 7s. Last read position: chr10:132,730,123 INFO 2016-11-10 20:04:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:04:46 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 8s. Last read position: chr11:35,359,267 INFO 2016-11-10 20:04:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:06 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 19s. Last read position: chr11:75,696,431 INFO 2016-11-10 20:05:06 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:05:26 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 20s. Last read position: chr11:114,414,621 INFO 2016-11-10 20:05:26 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:05:34 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 8s. Last read position: chr12:8,900,276 INFO 2016-11-10 20:05:34 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:05:42 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 7s. Last read position: chr12:38,863,889 INFO 2016-11-10 20:05:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:05:48 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 6s. Last read position: chr12:60,598,824 INFO 2016-11-10 20:05:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:05:54 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 5s. Last read position: chr12:88,520,538 INFO 2016-11-10 20:05:54 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:06:04 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 10s. Last read position: chr12:112,268,437 INFO 2016-11-10 20:06:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:11 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 7s. Last read position: chr13:23,999,632 INFO 2016-11-10 20:06:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:06:27 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 16s. Last read position: chr13:51,165,870 INFO 2016-11-10 20:06:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:06:35 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 7s. Last read position: chr13:88,986,369 INFO 2016-11-10 20:06:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:42 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 7s. Last read position: chr14:23,149,367 INFO 2016-11-10 20:06:42 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:06:50 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 7s. Last read position: chr14:58,140,905 INFO 2016-11-10 20:06:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:06:57 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 6s. Last read position: chr14:91,912,553 INFO 2016-11-10 20:06:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:07:05 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 8s. Last read position: chr15:38,895,095 INFO 2016-11-10 20:07:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:07:12 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 6s. Last read position: chr15:68,188,367 INFO 2016-11-10 20:07:12 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:07:21 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 8s. Last read position: chr15:87,921,272 INFO 2016-11-10 20:07:21 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:07:38 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 16s. Last read position: chr16:11,143,813 INFO 2016-11-10 20:07:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:07:44 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 6s. Last read position: chr16:51,391,437 INFO 2016-11-10 20:07:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:07:50 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 6s. Last read position: chr16:84,928,458 INFO 2016-11-10 20:07:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:07:59 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 8s. Last read position: chr17:18,368,935 INFO 2016-11-10 20:07:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:08:08 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 8s. Last read position: chr17:44,246,522 INFO 2016-11-10 20:08:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:08:18 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 10s. Last read position: chr17:66,172,158 INFO 2016-11-10 20:08:18 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 20:08:23 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 4s. Last read position: chr18:5,619,614 INFO 2016-11-10 20:08:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:08:29 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 6s. Last read position: chr18:46,152,631 INFO 2016-11-10 20:08:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:08:51 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 21s. Last read position: chr19:1,328,731 INFO 2016-11-10 20:08:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:09:01 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 9s. Last read position: chr19:28,148,444 INFO 2016-11-10 20:09:01 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:09:08 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 6s. Last read position: chr19:40,341,579 INFO 2016-11-10 20:09:08 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:09:15 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 7s. Last read position: chr20:3,222,035 INFO 2016-11-10 20:09:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:09:24 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 9s. Last read position: chr20:37,218,903 INFO 2016-11-10 20:09:24 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:10:23 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 58s. Last read position: chr20:62,871,367 INFO 2016-11-10 20:10:23 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-11-10 20:10:32 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 9s. Last read position: chr21:39,474,524 INFO 2016-11-10 20:10:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:10:41 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 8s. Last read position: chr22:31,346,944 INFO 2016-11-10 20:10:41 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-11-10 20:10:50 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 9s. Last read position: chrX:6,235,951 INFO 2016-11-10 20:10:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:10:56 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:15:16s. Time for last 1,000,000: 5s. Last read position: chrX:38,820,975 INFO 2016-11-10 20:10:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-11-10 20:11:05 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 8s. Last read position: chrX:69,473,954 INFO 2016-11-10 20:11:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:11:12 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:15:32s. Time for last 1,000,000: 6s. Last read position: chrX:92,683,143 INFO 2016-11-10 20:11:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-11-10 20:11:17 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:15:38s. Time for last 1,000,000: 5s. Last read position: chrX:118,447,518 INFO 2016-11-10 20:11:17 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-11-10 20:11:23 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 5s. Last read position: chrX:142,819,613 INFO 2016-11-10 20:11:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:11:30 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 6s. Last read position: chrM:3,995 INFO 2016-11-10 20:11:30 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM. INFO 2016-11-10 20:11:36 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:15:56s. Time for last 1,000,000: 5s. Last read position: chrM:11,775 INFO 2016-11-10 20:11:36 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM. INFO 2016-11-10 20:11:42 MarkDuplicates Read 99989486 records. 0 pairs never matched. INFO 2016-11-10 20:12:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 5774178016; totalMemory: 5853675520; maxMemory: 11453595648 INFO 2016-11-10 20:12:43 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 20:12:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 20:13:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 20:14:11 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 20:14:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 5767176600; totalMemory: 8708423680; maxMemory: 11453595648 INFO 2016-11-10 20:14:12 MarkDuplicates Marking 496224 records as duplicates. INFO 2016-11-10 20:14:12 MarkDuplicates Found 42648 optical duplicate clusters. INFO 2016-11-10 20:17:03 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:45s. Time for last 10,000,000: 165s. Last read position: chr2:3,652,468 INFO 2016-11-10 20:19:59 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:05:41s. Time for last 10,000,000: 176s. Last read position: chr3:128,121,129 INFO 2016-11-10 20:23:01 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:08:43s. Time for last 10,000,000: 181s. Last read position: chr5:86,336,676 INFO 2016-11-10 20:26:05 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:11:47s. Time for last 10,000,000: 184s. Last read position: chr6:156,918,595 INFO 2016-11-10 20:29:04 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:14:46s. Time for last 10,000,000: 178s. Last read position: chr9:18,183,883 INFO 2016-11-10 20:32:16 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:17:59s. Time for last 10,000,000: 192s. Last read position: chr11:75,696,431 INFO 2016-11-10 20:35:27 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:21:09s. Time for last 10,000,000: 190s. Last read position: chr14:23,149,367 INFO 2016-11-10 20:38:35 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:24:17s. Time for last 10,000,000: 188s. Last read position: chr17:44,246,522 INFO 2016-11-10 20:41:33 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:27:15s. Time for last 10,000,000: 178s. Last read position: chr21:39,474,524 INFO 2016-11-10 20:44:28 MarkDuplicates Before output close freeMemory: 8771921384; totalMemory: 8857845760; maxMemory: 11453595648 INFO 2016-11-10 20:44:30 MarkDuplicates After output close freeMemory: 8771920328; totalMemory: 8857845760; maxMemory: 11453595648 [Thu Nov 10 20:44:30 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 48.92 minutes. Runtime.totalMemory()=8857845760 | ||||||||||||||||||||||||||||||||||||||||
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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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21983 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Thu Nov 10 20:02:46 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_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 20:02:46 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 20:09:29 MarkDuplicates Start of doWork freeMemory: 254877880; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-10 20:09:29 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-10 20:09:29 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-10 20:15:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 28s. Last read position: chr1:177,028,049 INFO 2016-11-10 20:15:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:16:19 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 21s. Last read position: chr2:103,069,754 INFO 2016-11-10 20:16:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:16:42 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 22s. Last read position: chr3:65,385,965 INFO 2016-11-10 20:16:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:16:59 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 17s. Last read position: chr4:99,133,727 INFO 2016-11-10 20:16:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:17:24 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 25s. Last read position: chr5:85,406,409 INFO 2016-11-10 20:17:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:17:50 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 26s. Last read position: chr6:61,024,542 INFO 2016-11-10 20:17:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:18:13 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 22s. Last read position: chr7:55,616,792 INFO 2016-11-10 20:18:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:18:34 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 21s. Last read position: chr8:93,018,682 INFO 2016-11-10 20:18:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:18:54 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 20s. Last read position: chr10:35,380,048 INFO 2016-11-10 20:18:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:19:12 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 17s. Last read position: chr11:91,060,536 INFO 2016-11-10 20:19:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:22:18 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 186s. Last read position: chr12:125,618,179 INFO 2016-11-10 20:22:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:23:11 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 52s. Last read position: chr14:98,261,906 INFO 2016-11-10 20:23:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:23:49 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 38s. Last read position: chr17:17,781,294 INFO 2016-11-10 20:23:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:24:44 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 55s. Last read position: chr19:38,168,432 INFO 2016-11-10 20:24:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:26:08 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 84s. Last read position: chrX:13,284,465 INFO 2016-11-10 20:26:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:26:46 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 37s. Last read position: chrX:150,852,717 INFO 2016-11-10 20:26:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-10 20:26:48 MarkDuplicates Read 16070060 records. 0 pairs never matched. INFO 2016-11-10 20:26:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 4231181416; totalMemory: 5690621952; maxMemory: 11453595648 INFO 2016-11-10 20:26:54 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-10 20:26:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-10 20:26:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-10 20:26:58 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-10 20:30:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 5613913528; totalMemory: 8555331584; maxMemory: 11453595648 INFO 2016-11-10 20:30:45 MarkDuplicates Marking 2484471 records as duplicates. INFO 2016-11-10 20:30:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-11 00:17:46 MarkDuplicates Written 10,000,000 records. Elapsed time: 03:40:12s. Time for last 10,000,000: 13,212s. Last read position: chr11:91,060,536 INFO 2016-11-11 01:12:06 MarkDuplicates Before output close freeMemory: 8489788936; totalMemory: 8571060224; maxMemory: 11453595648 INFO 2016-11-11 01:13:23 MarkDuplicates After output close freeMemory: 8345082448; totalMemory: 8426356736; maxMemory: 11453595648 [Fri Nov 11 01:13:41 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 310.91 minutes. Runtime.totalMemory()=8426356736 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_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/SRR1370906_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/SRR1370906_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-------------------- 26478 (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/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 22956 (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/SRR1370906_1/out/align/rep1/SRR1370906_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_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/SRR1370906_1/out/qc/rep1/SRR1370906_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-------------------- 30796 (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/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 35001 (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 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 31357 (process ID) old priority 0, new priority 10 Waiting for 30 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr2/SRR1370906_1.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/pseudo_reps/rep1/pr1/SRR1370906_1.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 35168 (process ID) old priority 0, new priority 10 Waiting for 12 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 214
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_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--------------------
1924 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_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/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/align/rep1/SRR1370906_1.nodup.15M.tagAlign.gz
opened /tmp/7997.1.q/RtmpAAwsqm/SRR1370906_1.nodup.15M.tagAlign7c614a3d626
done. read 13575929 fragments
ChIP data read length 51
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1585487
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.181391700539729
Top 3 estimates for fragment length 140
Window half size 210
Phantom peak location 55
Phantom peak Correlation 0.1665981
Normalized Strand cross-correlation coefficient (NSC) 1.144076
Relative Strand cross-correlation Coefficient (RSC) 2.83786
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
Loading required package: caTools
Warning message:
package ‘caTools’ was built under R version 3.2.3
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# SYS command. line 98
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/report/SRR1370906_1_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/report/SRR1370906_1_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/report/SRR1370906_1_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 11882 (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/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out/qc/rep1/SRR1370906_1.nodup.15M.cc.plot.pdf
--------------------Stdout-------------------- 11918 (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, SRR1370906_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370906_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370906_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/SRR1370906_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/SRR1370906_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 | 32625.SRR1370906_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 |