| Script file | /users/pangwei/bds_atac/atac.bds |
|---|---|
| Program ID | atac.bds.20160517_165228_588 |
| Start time | 2016-05-17 16:52:28 |
| Run time | 1 day 18:48:56.934 |
| Tasks executed | 40 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19] |
| System* | local |
| Cpus* | 1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | atac.bds.20160517_165228_588/task.postalign_bed.pool_tag_reps.line_405.id_17 atac.bds.20160517_165228_588/task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_18 atac.bds.20160517_165228_588/task.callpeak_macs2.macs2_atac_pooled.line_192.id_19 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_20 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_rep1.line_25.id_21 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_22 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_rep2.line_25.id_23 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_24 atac.bds.20160517_165228_588/task.callpeak_etc.filt_top_peaks_pooled.line_25.id_25 atac.bds.20160517_165228_588/task.callpeak_etc.naive_overlap_thresh_peak.line_136.id_26 atac.bds.20160517_165228_588/task.callpeak_etc.naive_overlap_thresh_gpeak.line_136.id_27 atac.bds.20160517_165228_588/task.idr.idr2_rep1_rep2.line_72.id_28 atac.bds.20160517_165228_588/task.base.line_414.id_31 atac.bds.20160517_165228_588/task.base.line_414.id_32 atac.bds.20160517_165228_588/task.base.line_414.id_33 atac.bds.20160517_165228_588/task.base.line_414.id_34 atac.bds.20160517_165228_588/task.idr.idr_final_qc.line_210.id_35 atac.bds.20160517_165228_588/task.report.line_417.id_40 atac.bds.20160517_165228_588/task.report.line_417.id_41 atac.bds.20160517_165228_588/task.report.line_417.id_42 atac.bds.20160517_165228_588/task.report.line_417.id_43 atac.bds.20160517_165228_588/task.report.line_417.id_44 atac.bds.20160517_165228_588/task.report_graphviz.line_91.id_45 atac.bds.20160517_165228_588/task.report.line_382.id_50 atac.bds.20160517_165228_588/task.report.line_382.id_51 |
| thread_66 | thread_Root | atac.bds.20160517_165228_588_parallel_66/task.postalign_bam.srt_bam_rep1.line_345.id_36 atac.bds.20160517_165228_588_parallel_66/task.atac.ataqc_rep1.line_846.id_39 |
| thread_67 | thread_Root | atac.bds.20160517_165228_588_parallel_67/task.postalign_bam.srt_bam_rep2.line_345.id_37 atac.bds.20160517_165228_588_parallel_67/task.atac.ataqc_rep2.line_846.id_38 |
| thread_21 | thread_Root | |
| thread_20 | thread_Root | atac.bds.20160517_165228_588_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6 atac.bds.20160517_165228_588_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_7 atac.bds.20160517_165228_588_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_8 atac.bds.20160517_165228_588_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_9 atac.bds.20160517_165228_588_parallel_20/task.postalign_bed.subsample_bedpe_rep1.line_116.id_10 atac.bds.20160517_165228_588_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_11 atac.bds.20160517_165228_588_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_12 atac.bds.20160517_165228_588_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_13 atac.bds.20160517_165228_588_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_14 atac.bds.20160517_165228_588_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_15 atac.bds.20160517_165228_588_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_16 |
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# SYS command. line 133
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 135
bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.align.log | \
sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
echo
# SYS command. line 229
samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark
# SYS command. line 230
echo
# SYS command. line 237
samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 243
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 244
export MAX_JAVA_MEM="12G"
# SYS command. line 247
if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
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{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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam
--------------------Stdout-------------------- --------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 217 files... [bam_sort_core] merging from 222 files... Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed May 18 21:15:42 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.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 [Wed May 18 21:15:42 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-05-18 21:15:42 MarkDuplicates Start of doWork freeMemory: 254889656; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-05-18 21:15:42 MarkDuplicates Reading input file and constructing read end information. INFO 2016-05-18 21:15:42 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-05-18 21:15:48 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr10:13,768,867 INFO 2016-05-18 21:15:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:15:53 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 4s. Last read position: chr10:29,365,966 INFO 2016-05-18 21:15:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:15:56 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr10:48,551,607 INFO 2016-05-18 21:15:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:01 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 4s. Last read position: chr10:66,088,211 INFO 2016-05-18 21:16:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:05 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 4s. Last read position: chr10:78,304,019 INFO 2016-05-18 21:16:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:16:13 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 7s. Last read position: chr10:91,391,716 INFO 2016-05-18 21:16:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:19 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 5s. Last read position: chr10:103,547,352 INFO 2016-05-18 21:16:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:23 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr10:116,109,601 INFO 2016-05-18 21:16:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:16:26 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: chr10:127,697,332 INFO 2016-05-18 21:16:26 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:16:31 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 4s. Last read position: chr11:2,008,719 INFO 2016-05-18 21:16:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:16:36 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 5s. Last read position: chr11:13,571,842 INFO 2016-05-18 21:16:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:40 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr11:28,984,272 INFO 2016-05-18 21:16:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:16:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 4s. Last read position: chr11:44,838,187 INFO 2016-05-18 21:16:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:16:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr11:61,860,440 INFO 2016-05-18 21:16:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:17:04 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 16s. Last read position: chr11:69,658,250 INFO 2016-05-18 21:17:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:17:08 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr11:80,196,983 INFO 2016-05-18 21:17:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:17:12 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr11:96,766,591 INFO 2016-05-18 21:17:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:17:15 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: chr11:113,149,167 INFO 2016-05-18 21:17:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:17:21 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 5s. Last read position: chr11:123,568,066 INFO 2016-05-18 21:17:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:17:24 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr12:329,850 INFO 2016-05-18 21:17:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:17:27 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr12:12,381,511 INFO 2016-05-18 21:17:27 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:17:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr12:28,343,256 INFO 2016-05-18 21:17:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:17:36 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 5s. Last read position: chr12:48,214,721 INFO 2016-05-18 21:17:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:17:40 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chr12:57,635,014 INFO 2016-05-18 21:17:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:17:44 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: chr12:72,955,471 INFO 2016-05-18 21:17:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:17:48 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 4s. Last read position: chr12:90,346,621 INFO 2016-05-18 21:17:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:17:54 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 5s. Last read position: chr12:105,018,161 INFO 2016-05-18 21:17:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:17:57 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 3s. Last read position: chr12:116,118,477 INFO 2016-05-18 21:17:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:18:00 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr12:126,185,030 INFO 2016-05-18 21:18:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:12 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 11s. Last read position: chr13:24,729,244 INFO 2016-05-18 21:18:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:18:16 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: chr13:39,744,308 INFO 2016-05-18 21:18:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:20 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr13:54,731,407 INFO 2016-05-18 21:18:20 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:24 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 4s. Last read position: chr13:74,687,188 INFO 2016-05-18 21:18:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:28 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: chr13:93,734,460 INFO 2016-05-18 21:18:28 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-05-18 21:18:31 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: chr13:108,877,651 INFO 2016-05-18 21:18:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:35 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr14:25,162,016 INFO 2016-05-18 21:18:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:18:38 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 3s. Last read position: chr14:42,812,852 INFO 2016-05-18 21:18:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:18:42 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: chr14:59,082,259 INFO 2016-05-18 21:18:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:18:45 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: chr14:72,389,509 INFO 2016-05-18 21:18:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 5s. Last read position: chr14:85,881,371 INFO 2016-05-18 21:18:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:18:54 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 3s. Last read position: chr14:98,203,056 INFO 2016-05-18 21:18:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:18:57 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chr15:20,557,251 INFO 2016-05-18 21:18:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:00 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 3s. Last read position: chr15:39,886,152 INFO 2016-05-18 21:19:00 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:03 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr15:53,503,473 INFO 2016-05-18 21:19:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:11 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 7s. Last read position: chr15:66,882,355 INFO 2016-05-18 21:19:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:15 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 4s. Last read position: chr15:77,395,579 INFO 2016-05-18 21:19:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:19:19 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 3s. Last read position: chr15:90,217,450 INFO 2016-05-18 21:19:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:22 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 3s. Last read position: chr16:325,171 INFO 2016-05-18 21:19:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:25 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 3s. Last read position: chr16:9,350,241 INFO 2016-05-18 21:19:25 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:28 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 3s. Last read position: chr16:23,791,883 INFO 2016-05-18 21:19:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:31 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr16:48,901,834 INFO 2016-05-18 21:19:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:19:35 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chr16:60,627,064 INFO 2016-05-18 21:19:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:40 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 5s. Last read position: chr16:73,097,018 INFO 2016-05-18 21:19:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:44 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 3s. Last read position: chr16:85,347,291 INFO 2016-05-18 21:19:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:47 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 3s. Last read position: chr17:3,342,623 INFO 2016-05-18 21:19:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:19:50 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 3s. Last read position: chr17:14,128,276 INFO 2016-05-18 21:19:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:19:54 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 3s. Last read position: chr17:28,778,210 INFO 2016-05-18 21:19:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:19:57 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 3s. Last read position: chr17:39,942,362 INFO 2016-05-18 21:19:57 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:08 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 10s. Last read position: chr17:48,760,405 INFO 2016-05-18 21:20:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:11 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 3s. Last read position: chr17:62,133,028 INFO 2016-05-18 21:20:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:15 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 3s. Last read position: chr17:73,710,827 INFO 2016-05-18 21:20:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:18 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 3s. Last read position: chr17:81,007,002 INFO 2016-05-18 21:20:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:20:21 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr18:13,726,718 INFO 2016-05-18 21:20:21 MarkDuplicates Tracking 18 as yet unmatched pairs. 18 records in RAM. INFO 2016-05-18 21:20:25 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 3s. Last read position: chr18:33,093,734 INFO 2016-05-18 21:20:25 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:20:28 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 3s. Last read position: chr18:47,018,253 INFO 2016-05-18 21:20:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:32 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 3s. Last read position: chr18:61,528,601 INFO 2016-05-18 21:20:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:20:35 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr18:77,557,836 INFO 2016-05-18 21:20:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:38 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr19:7,114,212 INFO 2016-05-18 21:20:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:20:42 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 4s. Last read position: chr19:16,703,840 INFO 2016-05-18 21:20:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:20:45 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr19:32,244,975 INFO 2016-05-18 21:20:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:49 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 3s. Last read position: chr19:42,493,966 INFO 2016-05-18 21:20:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:20:52 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 3s. Last read position: chr19:51,028,256 INFO 2016-05-18 21:20:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:20:55 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 3s. Last read position: chr1:569,907 INFO 2016-05-18 21:20:55 MarkDuplicates Tracking 22730 as yet unmatched pairs. 22730 records in RAM. INFO 2016-05-18 21:21:02 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 6s. Last read position: chr1:6,453,896 INFO 2016-05-18 21:21:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:21:05 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr1:16,752,513 INFO 2016-05-18 21:21:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:21:08 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr1:25,862,011 INFO 2016-05-18 21:21:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:11 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr1:35,124,282 INFO 2016-05-18 21:21:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:16 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 5s. Last read position: chr1:45,060,949 INFO 2016-05-18 21:21:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:21:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 3s. Last read position: chr1:56,539,845 INFO 2016-05-18 21:21:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:23 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 3s. Last read position: chr1:71,141,616 INFO 2016-05-18 21:21:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:21:26 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 3s. Last read position: chr1:88,152,420 INFO 2016-05-18 21:21:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:21:30 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr1:103,359,856 INFO 2016-05-18 21:21:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:21:33 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr1:118,107,938 INFO 2016-05-18 21:21:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:37 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 3s. Last read position: chr1:155,214,473 INFO 2016-05-18 21:21:37 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-05-18 21:21:40 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 3s. Last read position: chr1:167,189,418 INFO 2016-05-18 21:21:40 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-18 21:21:43 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 3s. Last read position: chr1:181,307,358 INFO 2016-05-18 21:21:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:50 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 6s. Last read position: chr1:198,563,809 INFO 2016-05-18 21:21:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:21:53 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr1:209,659,358 INFO 2016-05-18 21:21:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:04 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 10s. Last read position: chr1:223,906,159 INFO 2016-05-18 21:22:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:22:07 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 3s. Last read position: chr1:235,785,563 INFO 2016-05-18 21:22:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:22:10 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 3s. Last read position: chr20:1,261,907 INFO 2016-05-18 21:22:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:15 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 4s. Last read position: chr20:14,985,822 INFO 2016-05-18 21:22:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:22:20 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 5s. Last read position: chr20:30,458,051 INFO 2016-05-18 21:22:20 MarkDuplicates Tracking 14 as yet unmatched pairs. 14 records in RAM. INFO 2016-05-18 21:22:25 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 5s. Last read position: chr20:39,745,299 INFO 2016-05-18 21:22:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:22:30 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 5s. Last read position: chr20:50,278,865 INFO 2016-05-18 21:22:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:35 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 5s. Last read position: chr20:61,610,079 INFO 2016-05-18 21:22:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:22:40 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 5s. Last read position: chr21:25,708,575 INFO 2016-05-18 21:22:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:44 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 3s. Last read position: chr21:40,403,135 INFO 2016-05-18 21:22:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:47 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 3s. Last read position: chr22:19,409,603 INFO 2016-05-18 21:22:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:22:50 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 3s. Last read position: chr22:30,116,749 INFO 2016-05-18 21:22:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:22:53 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 3s. Last read position: chr22:39,927,337 INFO 2016-05-18 21:22:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:22:55 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr22:49,027,605 INFO 2016-05-18 21:22:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:23:02 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 6s. Last read position: chr2:9,557,131 INFO 2016-05-18 21:23:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:05 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 3s. Last read position: chr2:22,089,086 INFO 2016-05-18 21:23:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:23:08 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 3s. Last read position: chr2:34,205,543 INFO 2016-05-18 21:23:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:11 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 3s. Last read position: chr2:47,790,925 INFO 2016-05-18 21:23:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:16 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 4s. Last read position: chr2:63,413,534 INFO 2016-05-18 21:23:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:20 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 3s. Last read position: chr2:75,827,442 INFO 2016-05-18 21:23:20 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:23 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: chr2:97,286,253 INFO 2016-05-18 21:23:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:26 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 3s. Last read position: chr2:112,505,603 INFO 2016-05-18 21:23:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:29 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 3s. Last read position: chr2:127,399,777 INFO 2016-05-18 21:23:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:23:32 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 3s. Last read position: chr2:141,855,890 INFO 2016-05-18 21:23:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:23:35 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 3s. Last read position: chr2:159,158,533 INFO 2016-05-18 21:23:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:38 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 2s. Last read position: chr2:174,768,786 INFO 2016-05-18 21:23:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:23:41 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 3s. Last read position: chr2:191,166,040 INFO 2016-05-18 21:23:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:23:44 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 3s. Last read position: chr2:206,950,336 INFO 2016-05-18 21:23:44 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:23:47 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr2:220,586,652 INFO 2016-05-18 21:23:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:23:58 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 11s. Last read position: chr2:234,433,362 INFO 2016-05-18 21:23:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:02 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 3s. Last read position: chr3:2,114,707 INFO 2016-05-18 21:24:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:05 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 3s. Last read position: chr3:14,154,423 INFO 2016-05-18 21:24:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:08 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 3s. Last read position: chr3:28,964,307 INFO 2016-05-18 21:24:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:11 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 3s. Last read position: chr3:42,746,745 INFO 2016-05-18 21:24:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:24:14 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 3s. Last read position: chr3:52,548,622 INFO 2016-05-18 21:24:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:24:17 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 3s. Last read position: chr3:66,300,652 INFO 2016-05-18 21:24:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:24:20 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 3s. Last read position: chr3:83,369,068 INFO 2016-05-18 21:24:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:23 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 3s. Last read position: chr3:105,601,275 INFO 2016-05-18 21:24:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:24:27 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 3s. Last read position: chr3:121,977,709 INFO 2016-05-18 21:24:27 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:24:30 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 3s. Last read position: chr3:133,449,351 INFO 2016-05-18 21:24:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:33 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 2s. Last read position: chr3:147,875,447 INFO 2016-05-18 21:24:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:38 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 5s. Last read position: chr3:163,949,866 INFO 2016-05-18 21:24:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:24:41 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 3s. Last read position: chr3:180,546,126 INFO 2016-05-18 21:24:41 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:24:44 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr3:193,942,904 INFO 2016-05-18 21:24:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:24:51 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 6s. Last read position: chr4:5,935,964 INFO 2016-05-18 21:24:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:24:54 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 3s. Last read position: chr4:18,943,597 INFO 2016-05-18 21:24:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:24:58 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 3s. Last read position: chr4:37,244,826 INFO 2016-05-18 21:24:58 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:02 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 3s. Last read position: chr4:56,679,197 INFO 2016-05-18 21:25:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:05 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 3s. Last read position: chr4:75,908,853 INFO 2016-05-18 21:25:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:09 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 3s. Last read position: chr4:91,332,056 INFO 2016-05-18 21:25:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:13 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 3s. Last read position: chr4:109,083,273 INFO 2016-05-18 21:25:13 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:25:16 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 3s. Last read position: chr4:126,245,560 INFO 2016-05-18 21:25:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:20 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 3s. Last read position: chr4:144,358,491 INFO 2016-05-18 21:25:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:24 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 3s. Last read position: chr4:160,403,088 INFO 2016-05-18 21:25:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:30 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 6s. Last read position: chr4:178,460,274 INFO 2016-05-18 21:25:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:34 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 3s. Last read position: chr5:1,829,078 INFO 2016-05-18 21:25:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:37 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 3s. Last read position: chr5:15,916,340 INFO 2016-05-18 21:25:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:25:41 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 3s. Last read position: chr5:34,577,659 INFO 2016-05-18 21:25:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:51 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 10s. Last read position: chr5:54,541,789 INFO 2016-05-18 21:25:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:55 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 3s. Last read position: chr5:71,850,497 INFO 2016-05-18 21:25:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:25:58 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 3s. Last read position: chr5:87,157,907 INFO 2016-05-18 21:25:58 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:26:01 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 3s. Last read position: chr5:104,447,068 INFO 2016-05-18 21:26:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:05 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 3s. Last read position: chr5:120,535,602 INFO 2016-05-18 21:26:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:08 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 3s. Last read position: chr5:134,259,871 INFO 2016-05-18 21:26:08 MarkDuplicates Tracking 928 as yet unmatched pairs. 928 records in RAM. INFO 2016-05-18 21:26:11 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr5:139,118,347 INFO 2016-05-18 21:26:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:26:14 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 3s. Last read position: chr5:150,937,724 INFO 2016-05-18 21:26:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:26:18 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 3s. Last read position: chr5:165,820,350 INFO 2016-05-18 21:26:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:23 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 5s. Last read position: chr5:176,896,264 INFO 2016-05-18 21:26:23 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-18 21:26:26 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 3s. Last read position: chr6:7,345,401 INFO 2016-05-18 21:26:26 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:26:30 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 3s. Last read position: chr6:21,374,904 INFO 2016-05-18 21:26:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:33 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 3s. Last read position: chr6:33,792,760 INFO 2016-05-18 21:26:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:26:36 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 3s. Last read position: chr6:43,543,052 INFO 2016-05-18 21:26:36 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM. INFO 2016-05-18 21:26:40 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 3s. Last read position: chr6:58,777,943 INFO 2016-05-18 21:26:40 MarkDuplicates Tracking 14 as yet unmatched pairs. 14 records in RAM. INFO 2016-05-18 21:26:46 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 6s. Last read position: chr6:80,425,328 INFO 2016-05-18 21:26:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:26:50 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 3s. Last read position: chr6:97,518,705 INFO 2016-05-18 21:26:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:53 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 3s. Last read position: chr6:112,946,422 INFO 2016-05-18 21:26:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:26:57 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 3s. Last read position: chr6:129,850,208 INFO 2016-05-18 21:26:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:27:00 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 3s. Last read position: chr6:145,290,866 INFO 2016-05-18 21:27:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:04 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 3s. Last read position: chr6:159,046,200 INFO 2016-05-18 21:27:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:27:07 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 3s. Last read position: chr7:491,904 INFO 2016-05-18 21:27:07 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:27:11 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 3s. Last read position: chr7:11,628,901 INFO 2016-05-18 21:27:11 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:17 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 6s. Last read position: chr7:27,539,639 INFO 2016-05-18 21:27:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:21 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 3s. Last read position: chr7:41,571,777 INFO 2016-05-18 21:27:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:27:24 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 3s. Last read position: chr7:55,563,396 INFO 2016-05-18 21:27:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:27 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 3s. Last read position: chr7:75,865,553 INFO 2016-05-18 21:27:27 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:31 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 3s. Last read position: chr7:93,015,132 INFO 2016-05-18 21:27:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:34 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 3s. Last read position: chr7:105,714,426 INFO 2016-05-18 21:27:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:38 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 3s. Last read position: chr7:122,500,308 INFO 2016-05-18 21:27:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:48 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 10s. Last read position: chr7:135,831,048 INFO 2016-05-18 21:27:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:27:52 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 3s. Last read position: chr7:150,530,042 INFO 2016-05-18 21:27:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:27:55 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 3s. Last read position: chr8:3,005,766 INFO 2016-05-18 21:27:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:27:58 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 3s. Last read position: chr8:19,430,197 INFO 2016-05-18 21:27:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:02 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 3s. Last read position: chr8:31,808,843 INFO 2016-05-18 21:28:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:05 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 3s. Last read position: chr8:49,580,010 INFO 2016-05-18 21:28:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:09 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 3s. Last read position: chr8:65,831,612 INFO 2016-05-18 21:28:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:12 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 3s. Last read position: chr8:81,528,082 INFO 2016-05-18 21:28:12 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:28:18 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 5s. Last read position: chr8:98,350,914 INFO 2016-05-18 21:28:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:21 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 3s. Last read position: chr8:112,908,837 INFO 2016-05-18 21:28:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:24 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 3s. Last read position: chr8:128,353,028 INFO 2016-05-18 21:28:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:27 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 3s. Last read position: chr8:141,630,401 INFO 2016-05-18 21:28:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:28:31 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 3s. Last read position: chr9:5,633,158 INFO 2016-05-18 21:28:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:34 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 3s. Last read position: chr9:22,059,701 INFO 2016-05-18 21:28:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:41 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 7s. Last read position: chr9:37,335,281 INFO 2016-05-18 21:28:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:44 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 3s. Last read position: chr9:83,090,294 INFO 2016-05-18 21:28:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:48 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 3s. Last read position: chr9:96,900,829 INFO 2016-05-18 21:28:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:28:52 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 3s. Last read position: chr9:110,842,724 INFO 2016-05-18 21:28:52 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:28:55 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 3s. Last read position: chr9:124,079,463 INFO 2016-05-18 21:28:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:28:59 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 3s. Last read position: chr9:132,977,462 INFO 2016-05-18 21:28:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:29:02 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 3s. Last read position: chr9:140,323,136 INFO 2016-05-18 21:29:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:29:05 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 2s. Last read position: chrM:118 INFO 2016-05-18 21:29:05 MarkDuplicates Tracking 25370 as yet unmatched pairs. 25370 records in RAM. INFO 2016-05-18 21:29:08 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 3s. Last read position: chrM:334 INFO 2016-05-18 21:29:08 MarkDuplicates Tracking 26408 as yet unmatched pairs. 26408 records in RAM. INFO 2016-05-18 21:29:11 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 3s. Last read position: chrM:475 INFO 2016-05-18 21:29:11 MarkDuplicates Tracking 45088 as yet unmatched pairs. 45088 records in RAM. INFO 2016-05-18 21:29:17 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 6s. Last read position: chrM:543 INFO 2016-05-18 21:29:17 MarkDuplicates Tracking 43662 as yet unmatched pairs. 43662 records in RAM. INFO 2016-05-18 21:29:20 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 2s. Last read position: chrM:683 INFO 2016-05-18 21:29:20 MarkDuplicates Tracking 16400 as yet unmatched pairs. 16400 records in RAM. INFO 2016-05-18 21:29:23 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 2s. Last read position: chrM:779 INFO 2016-05-18 21:29:23 MarkDuplicates Tracking 19732 as yet unmatched pairs. 19732 records in RAM. INFO 2016-05-18 21:29:26 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 3s. Last read position: chrM:912 INFO 2016-05-18 21:29:26 MarkDuplicates Tracking 32446 as yet unmatched pairs. 32446 records in RAM. INFO 2016-05-18 21:29:29 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 2s. Last read position: chrM:1,254 INFO 2016-05-18 21:29:29 MarkDuplicates Tracking 31604 as yet unmatched pairs. 31604 records in RAM. INFO 2016-05-18 21:29:41 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 11s. Last read position: chrM:1,384 INFO 2016-05-18 21:29:41 MarkDuplicates Tracking 13120 as yet unmatched pairs. 13120 records in RAM. INFO 2016-05-18 21:29:43 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 2s. Last read position: chrM:1,541 INFO 2016-05-18 21:29:43 MarkDuplicates Tracking 27728 as yet unmatched pairs. 27728 records in RAM. INFO 2016-05-18 21:29:46 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chrM:1,712 INFO 2016-05-18 21:29:46 MarkDuplicates Tracking 1064 as yet unmatched pairs. 1064 records in RAM. INFO 2016-05-18 21:29:49 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 2s. Last read position: chrM:1,948 INFO 2016-05-18 21:29:49 MarkDuplicates Tracking 12842 as yet unmatched pairs. 12842 records in RAM. INFO 2016-05-18 21:29:51 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 2s. Last read position: chrM:2,139 INFO 2016-05-18 21:29:51 MarkDuplicates Tracking 28492 as yet unmatched pairs. 28492 records in RAM. INFO 2016-05-18 21:29:54 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 2s. Last read position: chrM:2,358 INFO 2016-05-18 21:29:54 MarkDuplicates Tracking 6052 as yet unmatched pairs. 6052 records in RAM. INFO 2016-05-18 21:29:57 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 2s. Last read position: chrM:2,555 INFO 2016-05-18 21:29:57 MarkDuplicates Tracking 15706 as yet unmatched pairs. 15706 records in RAM. INFO 2016-05-18 21:29:59 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 2s. Last read position: chrM:2,660 INFO 2016-05-18 21:29:59 MarkDuplicates Tracking 49726 as yet unmatched pairs. 49726 records in RAM. INFO 2016-05-18 21:30:02 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 2s. Last read position: chrM:2,766 INFO 2016-05-18 21:30:02 MarkDuplicates Tracking 37658 as yet unmatched pairs. 37658 records in RAM. INFO 2016-05-18 21:30:05 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 2s. Last read position: chrM:2,871 INFO 2016-05-18 21:30:05 MarkDuplicates Tracking 35470 as yet unmatched pairs. 35470 records in RAM. INFO 2016-05-18 21:30:10 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 4s. Last read position: chrM:2,999 INFO 2016-05-18 21:30:10 MarkDuplicates Tracking 38428 as yet unmatched pairs. 38428 records in RAM. INFO 2016-05-18 21:30:13 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 2s. Last read position: chrM:3,098 INFO 2016-05-18 21:30:13 MarkDuplicates Tracking 42300 as yet unmatched pairs. 42300 records in RAM. INFO 2016-05-18 21:30:15 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 2s. Last read position: chrM:3,216 INFO 2016-05-18 21:30:15 MarkDuplicates Tracking 73614 as yet unmatched pairs. 73614 records in RAM. INFO 2016-05-18 21:30:18 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chrM:3,334 INFO 2016-05-18 21:30:18 MarkDuplicates Tracking 61154 as yet unmatched pairs. 61154 records in RAM. INFO 2016-05-18 21:30:21 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 2s. Last read position: chrM:3,414 INFO 2016-05-18 21:30:21 MarkDuplicates Tracking 26952 as yet unmatched pairs. 26952 records in RAM. INFO 2016-05-18 21:30:27 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 6s. Last read position: chrM:3,488 INFO 2016-05-18 21:30:27 MarkDuplicates Tracking 34488 as yet unmatched pairs. 34488 records in RAM. INFO 2016-05-18 21:30:30 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 2s. Last read position: chrM:3,575 INFO 2016-05-18 21:30:30 MarkDuplicates Tracking 99570 as yet unmatched pairs. 99570 records in RAM. INFO 2016-05-18 21:30:32 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 2s. Last read position: chrM:3,647 INFO 2016-05-18 21:30:32 MarkDuplicates Tracking 30954 as yet unmatched pairs. 30954 records in RAM. INFO 2016-05-18 21:30:35 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 2s. Last read position: chrM:3,735 INFO 2016-05-18 21:30:35 MarkDuplicates Tracking 35064 as yet unmatched pairs. 35064 records in RAM. INFO 2016-05-18 21:30:38 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 2s. Last read position: chrM:3,857 INFO 2016-05-18 21:30:38 MarkDuplicates Tracking 29814 as yet unmatched pairs. 29814 records in RAM. INFO 2016-05-18 21:30:40 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 2s. Last read position: chrM:4,044 INFO 2016-05-18 21:30:40 MarkDuplicates Tracking 26782 as yet unmatched pairs. 26782 records in RAM. INFO 2016-05-18 21:30:43 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 2s. Last read position: chrM:4,382 INFO 2016-05-18 21:30:43 MarkDuplicates Tracking 8128 as yet unmatched pairs. 8128 records in RAM. INFO 2016-05-18 21:30:46 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 2s. Last read position: chrM:4,837 INFO 2016-05-18 21:30:46 MarkDuplicates Tracking 14424 as yet unmatched pairs. 14424 records in RAM. INFO 2016-05-18 21:30:48 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 2s. Last read position: chrM:4,951 INFO 2016-05-18 21:30:48 MarkDuplicates Tracking 14120 as yet unmatched pairs. 14120 records in RAM. INFO 2016-05-18 21:30:51 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 2s. Last read position: chrM:5,137 INFO 2016-05-18 21:30:51 MarkDuplicates Tracking 10802 as yet unmatched pairs. 10802 records in RAM. INFO 2016-05-18 21:30:53 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 2s. Last read position: chrM:5,377 INFO 2016-05-18 21:30:53 MarkDuplicates Tracking 5274 as yet unmatched pairs. 5274 records in RAM. INFO 2016-05-18 21:30:56 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 2s. Last read position: chrM:5,758 INFO 2016-05-18 21:30:56 MarkDuplicates Tracking 4784 as yet unmatched pairs. 4784 records in RAM. INFO 2016-05-18 21:31:02 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 6s. Last read position: chrM:6,018 INFO 2016-05-18 21:31:02 MarkDuplicates Tracking 8694 as yet unmatched pairs. 8694 records in RAM. INFO 2016-05-18 21:31:06 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 3s. Last read position: chrM:6,248 INFO 2016-05-18 21:31:06 MarkDuplicates Tracking 25280 as yet unmatched pairs. 25280 records in RAM. INFO 2016-05-18 21:31:18 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 12s. Last read position: chrM:6,340 INFO 2016-05-18 21:31:18 MarkDuplicates Tracking 13760 as yet unmatched pairs. 13760 records in RAM. INFO 2016-05-18 21:31:21 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:15:38s. Time for last 1,000,000: 3s. Last read position: chrM:6,434 INFO 2016-05-18 21:31:21 MarkDuplicates Tracking 45760 as yet unmatched pairs. 45760 records in RAM. INFO 2016-05-18 21:31:24 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:15:42s. Time for last 1,000,000: 3s. Last read position: chrM:6,527 INFO 2016-05-18 21:31:24 MarkDuplicates Tracking 23588 as yet unmatched pairs. 23588 records in RAM. INFO 2016-05-18 21:31:28 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 3s. Last read position: chrM:6,638 INFO 2016-05-18 21:31:28 MarkDuplicates Tracking 34406 as yet unmatched pairs. 34406 records in RAM. INFO 2016-05-18 21:31:31 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:15:48s. Time for last 1,000,000: 3s. Last read position: chrM:6,931 INFO 2016-05-18 21:31:31 MarkDuplicates Tracking 11578 as yet unmatched pairs. 11578 records in RAM. INFO 2016-05-18 21:31:34 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 3s. Last read position: chrM:7,192 INFO 2016-05-18 21:31:34 MarkDuplicates Tracking 13322 as yet unmatched pairs. 13322 records in RAM. INFO 2016-05-18 21:31:37 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 3s. Last read position: chrM:7,608 INFO 2016-05-18 21:31:37 MarkDuplicates Tracking 17896 as yet unmatched pairs. 17896 records in RAM. INFO 2016-05-18 21:31:41 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:15:58s. Time for last 1,000,000: 3s. Last read position: chrM:7,798 INFO 2016-05-18 21:31:41 MarkDuplicates Tracking 9874 as yet unmatched pairs. 9874 records in RAM. INFO 2016-05-18 21:31:44 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 3s. Last read position: chrM:7,893 INFO 2016-05-18 21:31:44 MarkDuplicates Tracking 36404 as yet unmatched pairs. 36404 records in RAM. INFO 2016-05-18 21:31:47 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 3s. Last read position: chrM:8,061 INFO 2016-05-18 21:31:47 MarkDuplicates Tracking 10896 as yet unmatched pairs. 10896 records in RAM. INFO 2016-05-18 21:31:53 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 5s. Last read position: chrM:8,173 INFO 2016-05-18 21:31:53 MarkDuplicates Tracking 8262 as yet unmatched pairs. 8262 records in RAM. INFO 2016-05-18 21:31:56 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:16:13s. Time for last 1,000,000: 3s. Last read position: chrM:8,461 INFO 2016-05-18 21:31:56 MarkDuplicates Tracking 15598 as yet unmatched pairs. 15598 records in RAM. INFO 2016-05-18 21:31:59 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 3s. Last read position: chrM:8,712 INFO 2016-05-18 21:31:59 MarkDuplicates Tracking 12896 as yet unmatched pairs. 12896 records in RAM. INFO 2016-05-18 21:32:02 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 3s. Last read position: chrM:9,144 INFO 2016-05-18 21:32:02 MarkDuplicates Tracking 4326 as yet unmatched pairs. 4326 records in RAM. INFO 2016-05-18 21:32:05 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 3s. Last read position: chrM:9,283 INFO 2016-05-18 21:32:05 MarkDuplicates Tracking 26664 as yet unmatched pairs. 26664 records in RAM. INFO 2016-05-18 21:32:12 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 7s. Last read position: chrM:9,522 INFO 2016-05-18 21:32:12 MarkDuplicates Tracking 7634 as yet unmatched pairs. 7634 records in RAM. INFO 2016-05-18 21:32:16 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 3s. Last read position: chrM:9,745 INFO 2016-05-18 21:32:16 MarkDuplicates Tracking 43454 as yet unmatched pairs. 43454 records in RAM. INFO 2016-05-18 21:32:19 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 3s. Last read position: chrM:9,856 INFO 2016-05-18 21:32:19 MarkDuplicates Tracking 40368 as yet unmatched pairs. 40368 records in RAM. INFO 2016-05-18 21:32:22 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 3s. Last read position: chrM:10,006 INFO 2016-05-18 21:32:22 MarkDuplicates Tracking 48328 as yet unmatched pairs. 48328 records in RAM. INFO 2016-05-18 21:32:25 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 3s. Last read position: chrM:10,185 INFO 2016-05-18 21:32:25 MarkDuplicates Tracking 30522 as yet unmatched pairs. 30522 records in RAM. INFO 2016-05-18 21:32:29 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 3s. Last read position: chrM:10,308 INFO 2016-05-18 21:32:29 MarkDuplicates Tracking 16276 as yet unmatched pairs. 16276 records in RAM. INFO 2016-05-18 21:32:32 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:16:49s. Time for last 1,000,000: 3s. Last read position: chrM:10,523 INFO 2016-05-18 21:32:32 MarkDuplicates Tracking 2170 as yet unmatched pairs. 2170 records in RAM. INFO 2016-05-18 21:32:35 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 3s. Last read position: chrM:10,640 INFO 2016-05-18 21:32:35 MarkDuplicates Tracking 14442 as yet unmatched pairs. 14442 records in RAM. INFO 2016-05-18 21:32:38 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 3s. Last read position: chrM:10,745 INFO 2016-05-18 21:32:38 MarkDuplicates Tracking 33418 as yet unmatched pairs. 33418 records in RAM. INFO 2016-05-18 21:32:41 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 3s. Last read position: chrM:11,124 INFO 2016-05-18 21:32:41 MarkDuplicates Tracking 6332 as yet unmatched pairs. 6332 records in RAM. INFO 2016-05-18 21:32:44 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 3s. Last read position: chrM:11,219 INFO 2016-05-18 21:32:44 MarkDuplicates Tracking 744 as yet unmatched pairs. 744 records in RAM. INFO 2016-05-18 21:32:48 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 3s. Last read position: chrM:11,357 INFO 2016-05-18 21:32:48 MarkDuplicates Tracking 4814 as yet unmatched pairs. 4814 records in RAM. INFO 2016-05-18 21:32:51 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:17:08s. Time for last 1,000,000: 3s. Last read position: chrM:11,539 INFO 2016-05-18 21:32:51 MarkDuplicates Tracking 4232 as yet unmatched pairs. 4232 records in RAM. INFO 2016-05-18 21:32:54 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:17:11s. Time for last 1,000,000: 3s. Last read position: chrM:11,738 INFO 2016-05-18 21:32:54 MarkDuplicates Tracking 7074 as yet unmatched pairs. 7074 records in RAM. INFO 2016-05-18 21:33:01 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 6s. Last read position: chrM:11,919 INFO 2016-05-18 21:33:01 MarkDuplicates Tracking 1580 as yet unmatched pairs. 1580 records in RAM. INFO 2016-05-18 21:33:14 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:17:31s. Time for last 1,000,000: 12s. Last read position: chrM:12,016 INFO 2016-05-18 21:33:14 MarkDuplicates Tracking 22440 as yet unmatched pairs. 22440 records in RAM. INFO 2016-05-18 21:33:17 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:17:34s. Time for last 1,000,000: 2s. Last read position: chrM:12,147 INFO 2016-05-18 21:33:17 MarkDuplicates Tracking 5172 as yet unmatched pairs. 5172 records in RAM. INFO 2016-05-18 21:33:19 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 2s. Last read position: chrM:12,354 INFO 2016-05-18 21:33:19 MarkDuplicates Tracking 40386 as yet unmatched pairs. 40386 records in RAM. INFO 2016-05-18 21:33:22 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 3s. Last read position: chrM:12,497 INFO 2016-05-18 21:33:22 MarkDuplicates Tracking 16792 as yet unmatched pairs. 16792 records in RAM. INFO 2016-05-18 21:33:25 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:17:43s. Time for last 1,000,000: 3s. Last read position: chrM:12,599 INFO 2016-05-18 21:33:25 MarkDuplicates Tracking 33534 as yet unmatched pairs. 33534 records in RAM. INFO 2016-05-18 21:33:29 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 3s. Last read position: chrM:12,720 INFO 2016-05-18 21:33:29 MarkDuplicates Tracking 14432 as yet unmatched pairs. 14432 records in RAM. INFO 2016-05-18 21:33:32 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 2s. Last read position: chrM:12,929 INFO 2016-05-18 21:33:32 MarkDuplicates Tracking 1462 as yet unmatched pairs. 1462 records in RAM. INFO 2016-05-18 21:33:35 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:17:52s. Time for last 1,000,000: 2s. Last read position: chrM:13,028 INFO 2016-05-18 21:33:35 MarkDuplicates Tracking 26084 as yet unmatched pairs. 26084 records in RAM. INFO 2016-05-18 21:33:38 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:17:55s. Time for last 1,000,000: 3s. Last read position: chrM:13,108 INFO 2016-05-18 21:33:38 MarkDuplicates Tracking 46698 as yet unmatched pairs. 46698 records in RAM. INFO 2016-05-18 21:33:41 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:17:58s. Time for last 1,000,000: 2s. Last read position: chrM:13,206 INFO 2016-05-18 21:33:41 MarkDuplicates Tracking 22552 as yet unmatched pairs. 22552 records in RAM. INFO 2016-05-18 21:33:47 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:18:04s. Time for last 1,000,000: 5s. Last read position: chrM:13,347 INFO 2016-05-18 21:33:47 MarkDuplicates Tracking 14676 as yet unmatched pairs. 14676 records in RAM. INFO 2016-05-18 21:33:50 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 3s. Last read position: chrM:13,458 INFO 2016-05-18 21:33:50 MarkDuplicates Tracking 21184 as yet unmatched pairs. 21184 records in RAM. INFO 2016-05-18 21:33:53 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 3s. Last read position: chrM:13,577 INFO 2016-05-18 21:33:53 MarkDuplicates Tracking 19036 as yet unmatched pairs. 19036 records in RAM. INFO 2016-05-18 21:33:57 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:18:14s. Time for last 1,000,000: 3s. Last read position: chrM:13,687 INFO 2016-05-18 21:33:57 MarkDuplicates Tracking 43252 as yet unmatched pairs. 43252 records in RAM. INFO 2016-05-18 21:34:04 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:18:21s. Time for last 1,000,000: 7s. Last read position: chrM:13,838 INFO 2016-05-18 21:34:04 MarkDuplicates Tracking 44372 as yet unmatched pairs. 44372 records in RAM. INFO 2016-05-18 21:34:07 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 3s. Last read position: chrM:13,954 INFO 2016-05-18 21:34:07 MarkDuplicates Tracking 21642 as yet unmatched pairs. 21642 records in RAM. INFO 2016-05-18 21:34:10 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:18:28s. Time for last 1,000,000: 3s. Last read position: chrM:14,090 INFO 2016-05-18 21:34:10 MarkDuplicates Tracking 1300 as yet unmatched pairs. 1300 records in RAM. INFO 2016-05-18 21:34:13 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 3s. Last read position: chrM:14,309 INFO 2016-05-18 21:34:13 MarkDuplicates Tracking 27992 as yet unmatched pairs. 27992 records in RAM. INFO 2016-05-18 21:34:16 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:18:34s. Time for last 1,000,000: 2s. Last read position: chrM:14,405 INFO 2016-05-18 21:34:16 MarkDuplicates Tracking 15226 as yet unmatched pairs. 15226 records in RAM. INFO 2016-05-18 21:34:19 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:18:37s. Time for last 1,000,000: 2s. Last read position: chrM:14,602 INFO 2016-05-18 21:34:19 MarkDuplicates Tracking 2254 as yet unmatched pairs. 2254 records in RAM. INFO 2016-05-18 21:34:22 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 2s. Last read position: chrM:14,823 INFO 2016-05-18 21:34:22 MarkDuplicates Tracking 4632 as yet unmatched pairs. 4632 records in RAM. INFO 2016-05-18 21:34:25 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 2s. Last read position: chrM:14,991 INFO 2016-05-18 21:34:25 MarkDuplicates Tracking 40740 as yet unmatched pairs. 40740 records in RAM. INFO 2016-05-18 21:34:28 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 2s. Last read position: chrM:15,094 INFO 2016-05-18 21:34:28 MarkDuplicates Tracking 15400 as yet unmatched pairs. 15400 records in RAM. INFO 2016-05-18 21:34:31 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:18:48s. Time for last 1,000,000: 2s. Last read position: chrM:15,181 INFO 2016-05-18 21:34:31 MarkDuplicates Tracking 12676 as yet unmatched pairs. 12676 records in RAM. INFO 2016-05-18 21:34:34 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 2s. Last read position: chrM:15,269 INFO 2016-05-18 21:34:34 MarkDuplicates Tracking 17088 as yet unmatched pairs. 17088 records in RAM. INFO 2016-05-18 21:34:37 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 2s. Last read position: chrM:15,376 INFO 2016-05-18 21:34:37 MarkDuplicates Tracking 26682 as yet unmatched pairs. 26682 records in RAM. INFO 2016-05-18 21:34:40 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 2s. Last read position: chrM:15,480 INFO 2016-05-18 21:34:40 MarkDuplicates Tracking 34714 as yet unmatched pairs. 34714 records in RAM. INFO 2016-05-18 21:34:43 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:19:00s. Time for last 1,000,000: 2s. Last read position: chrM:15,575 INFO 2016-05-18 21:34:43 MarkDuplicates Tracking 45038 as yet unmatched pairs. 45038 records in RAM. INFO 2016-05-18 21:34:49 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:19:07s. Time for last 1,000,000: 6s. Last read position: chrM:15,665 INFO 2016-05-18 21:34:49 MarkDuplicates Tracking 56854 as yet unmatched pairs. 56854 records in RAM. INFO 2016-05-18 21:35:03 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 13s. Last read position: chrM:15,748 INFO 2016-05-18 21:35:03 MarkDuplicates Tracking 38126 as yet unmatched pairs. 38126 records in RAM. INFO 2016-05-18 21:35:06 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 2s. Last read position: chrM:15,841 INFO 2016-05-18 21:35:06 MarkDuplicates Tracking 39386 as yet unmatched pairs. 39386 records in RAM. INFO 2016-05-18 21:35:08 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 2s. Last read position: chrM:15,991 INFO 2016-05-18 21:35:08 MarkDuplicates Tracking 34756 as yet unmatched pairs. 34756 records in RAM. INFO 2016-05-18 21:35:11 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 2s. Last read position: chrM:16,255 INFO 2016-05-18 21:35:11 MarkDuplicates Tracking 16788 as yet unmatched pairs. 16788 records in RAM. INFO 2016-05-18 21:35:14 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 2s. Last read position: chrM:16,364 INFO 2016-05-18 21:35:14 MarkDuplicates Tracking 15190 as yet unmatched pairs. 15190 records in RAM. INFO 2016-05-18 21:35:17 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:19:34s. Time for last 1,000,000: 2s. Last read position: chrM:16,439 INFO 2016-05-18 21:35:17 MarkDuplicates Tracking 13942 as yet unmatched pairs. 13942 records in RAM. INFO 2016-05-18 21:35:19 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 2s. Last read position: chrX:5,820,230 INFO 2016-05-18 21:35:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:35:22 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:19:40s. Time for last 1,000,000: 2s. Last read position: chrX:19,998,042 INFO 2016-05-18 21:35:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:35:25 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 3s. Last read position: chrX:37,545,245 INFO 2016-05-18 21:35:25 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-18 21:35:28 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:19:46s. Time for last 1,000,000: 3s. Last read position: chrX:51,985,699 INFO 2016-05-18 21:35:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:35:33 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 5s. Last read position: chrX:73,641,118 INFO 2016-05-18 21:35:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:35:37 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:19:54s. Time for last 1,000,000: 3s. Last read position: chrX:96,647,676 INFO 2016-05-18 21:35:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:35:40 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:19:57s. Time for last 1,000,000: 3s. Last read position: chrX:112,610,470 INFO 2016-05-18 21:35:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-18 21:35:43 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:20:00s. Time for last 1,000,000: 3s. Last read position: chrX:129,255,119 INFO 2016-05-18 21:35:43 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-18 21:35:46 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:20:03s. Time for last 1,000,000: 3s. Last read position: chrX:145,269,144 INFO 2016-05-18 21:35:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-18 21:35:52 MarkDuplicates Read 308685482 records. 0 pairs never matched. INFO 2016-05-18 21:35:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 4090007192; totalMemory: 4117757952; maxMemory: 4117757952 INFO 2016-05-18 21:35:55 MarkDuplicates Will retain up to 128679936 duplicate indices before spilling to disk. INFO 2016-05-18 21:35:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-05-18 21:37:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-05-18 21:38:42 MarkDuplicates Sorting list of duplicate records. INFO 2016-05-18 21:38:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 4142460736; totalMemory: 4172283904; maxMemory: 4172283904 INFO 2016-05-18 21:38:43 MarkDuplicates Marking 143101150 records as duplicates. INFO 2016-05-18 21:38:43 MarkDuplicates Found 62470578 optical duplicate clusters. INFO 2016-05-18 21:40:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 84s. Last read position: chr11:2,008,719 INFO 2016-05-18 21:41:38 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:53s. Time for last 10,000,000: 89s. Last read position: chr12:329,850 INFO 2016-05-18 21:43:06 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:04:21s. Time for last 10,000,000: 88s. Last read position: chr13:24,729,244 INFO 2016-05-18 21:44:33 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:05:47s. Time for last 10,000,000: 86s. Last read position: chr14:85,881,371 INFO 2016-05-18 21:45:56 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 83s. Last read position: chr16:23,791,883 INFO 2016-05-18 21:47:19 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:08:34s. Time for last 10,000,000: 83s. Last read position: chr17:62,133,028 INFO 2016-05-18 21:48:43 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:09:58s. Time for last 10,000,000: 83s. Last read position: chr19:32,244,975 INFO 2016-05-18 21:50:05 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:11:20s. Time for last 10,000,000: 82s. Last read position: chr1:71,141,616 INFO 2016-05-18 21:51:30 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:12:45s. Time for last 10,000,000: 84s. Last read position: chr1:235,785,563 INFO 2016-05-18 21:52:53 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:14:08s. Time for last 10,000,000: 83s. Last read position: chr22:30,116,749 INFO 2016-05-18 21:54:17 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:15:32s. Time for last 10,000,000: 83s. Last read position: chr2:112,505,603 INFO 2016-05-18 21:55:45 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:17:00s. Time for last 10,000,000: 87s. Last read position: chr3:14,154,423 INFO 2016-05-18 21:57:11 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:18:25s. Time for last 10,000,000: 85s. Last read position: chr3:163,949,866 INFO 2016-05-18 21:58:37 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:19:51s. Time for last 10,000,000: 85s. Last read position: chr4:126,245,560 INFO 2016-05-18 22:00:03 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:21:17s. Time for last 10,000,000: 86s. Last read position: chr5:104,447,068 INFO 2016-05-18 22:01:26 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:22:40s. Time for last 10,000,000: 82s. Last read position: chr6:43,543,052 INFO 2016-05-18 22:02:51 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:24:06s. Time for last 10,000,000: 85s. Last read position: chr7:27,539,639 INFO 2016-05-18 22:04:17 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:25:32s. Time for last 10,000,000: 85s. Last read position: chr8:19,430,197 INFO 2016-05-18 22:05:42 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:26:57s. Time for last 10,000,000: 85s. Last read position: chr9:22,059,701 INFO 2016-05-18 22:07:02 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:28:17s. Time for last 10,000,000: 80s. Last read position: chrM:475 INFO 2016-05-18 22:08:09 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:29:24s. Time for last 10,000,000: 66s. Last read position: chrM:2,139 INFO 2016-05-18 22:09:17 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:30:31s. Time for last 10,000,000: 67s. Last read position: chrM:3,414 INFO 2016-05-18 22:10:22 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:31:37s. Time for last 10,000,000: 65s. Last read position: chrM:5,137 INFO 2016-05-18 22:11:27 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:32:42s. Time for last 10,000,000: 64s. Last read position: chrM:7,192 INFO 2016-05-18 22:12:32 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:33:46s. Time for last 10,000,000: 64s. Last read position: chrM:9,522 INFO 2016-05-18 22:13:38 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:34:52s. Time for last 10,000,000: 66s. Last read position: chrM:11,219 INFO 2016-05-18 22:14:43 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:35:58s. Time for last 10,000,000: 65s. Last read position: chrM:12,720 INFO 2016-05-18 22:15:49 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:37:03s. Time for last 10,000,000: 65s. Last read position: chrM:13,954 INFO 2016-05-18 22:16:53 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:38:08s. Time for last 10,000,000: 64s. Last read position: chrM:15,376 INFO 2016-05-18 22:18:01 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:39:16s. Time for last 10,000,000: 68s. Last read position: chrX:5,820,230 Could not delete file /tmp/pangwei/sortingcollection.2999365041918760077.tmp Could not delete file /tmp/pangwei/sortingcollection.7084992286918172623.tmp INFO 2016-05-18 22:19:15 MarkDuplicates Before output close freeMemory: 4158039552; totalMemory: 4188536832; maxMemory: 4188536832 INFO 2016-05-18 22:19:15 MarkDuplicates After output close freeMemory: 4158038736; totalMemory: 4188536832; maxMemory: 4188536832 [Wed May 18 22:19:15 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 63.56 minutes. Runtime.totalMemory()=4188536832 [bam_sort_core] merging from 223 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 323
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 325
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 119 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 427
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 430
bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 118
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 120
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 467
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 469
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
# SYS command. line 472
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 91
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
grep -v "chrM" | shuf -n 25000000 | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 167
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 171
Rscript $(which run_spp_nodups.R) -rf \
-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0
# SYS command. line 174
sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp
# SYS command. line 175
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 0
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
opened /tmp/RtmpHSBdxj/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign6b066a586233
done. read 25000000 fragments
ChIP data read length 63
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.2480135
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.265560858672526
Top 3 estimates for fragment length 0
Window half size 470
Phantom peak location 55
Phantom peak Correlation 0.2676213
Normalized Strand cross-correlation coefficient (NSC) 1.070752
Relative Strand Cross correlation Coefficient (RSC) 0.8949163
Phantom Peak Quality Tag 0
null device
1
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH INFO @ Thu, 19 May 2016 02:30:53: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff for narrow/strong regions = 1.00e-01 # pvalue cutoff for broad/weak regions = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is on INFO @ Thu, 19 May 2016 02:30:53: #1 read tag files... INFO @ Thu, 19 May 2016 02:30:53: #1 read treatment tags... INFO @ Thu, 19 May 2016 02:30:55: 1000000 INFO @ Thu, 19 May 2016 02:30:57: 2000000 INFO @ Thu, 19 May 2016 02:30:58: 3000000 INFO @ Thu, 19 May 2016 02:31:00: 4000000 INFO @ Thu, 19 May 2016 02:31:01: 5000000 INFO @ Thu, 19 May 2016 02:31:03: 6000000 INFO @ Thu, 19 May 2016 02:31:04: 7000000 INFO @ Thu, 19 May 2016 02:31:06: 8000000 INFO @ Thu, 19 May 2016 02:31:07: 9000000 INFO @ Thu, 19 May 2016 02:31:09: 10000000 INFO @ Thu, 19 May 2016 02:31:10: 11000000 INFO @ Thu, 19 May 2016 02:31:12: 12000000 INFO @ Thu, 19 May 2016 02:31:14: 13000000 INFO @ Thu, 19 May 2016 02:31:15: 14000000 INFO @ Thu, 19 May 2016 02:31:17: 15000000 INFO @ Thu, 19 May 2016 02:31:18: 16000000 INFO @ Thu, 19 May 2016 02:31:20: 17000000 INFO @ Thu, 19 May 2016 02:31:21: 18000000 INFO @ Thu, 19 May 2016 02:31:23: 19000000 INFO @ Thu, 19 May 2016 02:31:24: 20000000 INFO @ Thu, 19 May 2016 02:31:26: 21000000 INFO @ Thu, 19 May 2016 02:31:27: 22000000 INFO @ Thu, 19 May 2016 02:31:29: 23000000 INFO @ Thu, 19 May 2016 02:31:30: 24000000 INFO @ Thu, 19 May 2016 02:31:32: 25000000 INFO @ Thu, 19 May 2016 02:31:33: 26000000 INFO @ Thu, 19 May 2016 02:31:35: 27000000 INFO @ Thu, 19 May 2016 02:31:36: 28000000 INFO @ Thu, 19 May 2016 02:31:38: 29000000 INFO @ Thu, 19 May 2016 02:31:39: 30000000 INFO @ Thu, 19 May 2016 02:31:41: 31000000 INFO @ Thu, 19 May 2016 02:31:42: 32000000 INFO @ Thu, 19 May 2016 02:31:44: 33000000 INFO @ Thu, 19 May 2016 02:31:45: 34000000 INFO @ Thu, 19 May 2016 02:31:47: 35000000 INFO @ Thu, 19 May 2016 02:31:49: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 02:31:49: #1 tag size = 76 INFO @ Thu, 19 May 2016 02:31:49: #1 total tags in treatment: 35000000 INFO @ Thu, 19 May 2016 02:31:49: #1 finished! INFO @ Thu, 19 May 2016 02:31:49: #2 Build Peak Model... INFO @ Thu, 19 May 2016 02:31:49: #2 Skipped... INFO @ Thu, 19 May 2016 02:31:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 02:31:49: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 02:31:49: #3 Call peaks... INFO @ Thu, 19 May 2016 02:31:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... INFO @ Thu, 19 May 2016 02:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 02:32:51: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 02:34:55: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls INFO @ Thu, 19 May 2016 02:34:59: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak INFO @ Thu, 19 May 2016 02:35:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak INFO @ Thu, 19 May 2016 02:35:04: Done! INFO @ Thu, 19 May 2016 02:35:16: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Searching for subpeak summits is on # MACS will save fragment pileup signal per million reads INFO @ Thu, 19 May 2016 02:35:16: #1 read tag files... INFO @ Thu, 19 May 2016 02:35:16: #1 read treatment tags... INFO @ Thu, 19 May 2016 02:35:17: 1000000 INFO @ Thu, 19 May 2016 02:35:19: 2000000 INFO @ Thu, 19 May 2016 02:35:20: 3000000 INFO @ Thu, 19 May 2016 02:35:22: 4000000 INFO @ Thu, 19 May 2016 02:35:23: 5000000 INFO @ Thu, 19 May 2016 02:35:25: 6000000 INFO @ Thu, 19 May 2016 02:35:26: 7000000 INFO @ Thu, 19 May 2016 02:35:28: 8000000 INFO @ Thu, 19 May 2016 02:35:29: 9000000 INFO @ Thu, 19 May 2016 02:35:31: 10000000 INFO @ Thu, 19 May 2016 02:35:32: 11000000 INFO @ Thu, 19 May 2016 02:35:34: 12000000 INFO @ Thu, 19 May 2016 02:35:35: 13000000 INFO @ Thu, 19 May 2016 02:35:37: 14000000 INFO @ Thu, 19 May 2016 02:35:39: 15000000 INFO @ Thu, 19 May 2016 02:35:40: 16000000 INFO @ Thu, 19 May 2016 02:35:42: 17000000 INFO @ Thu, 19 May 2016 02:35:43: 18000000 INFO @ Thu, 19 May 2016 02:35:45: 19000000 INFO @ Thu, 19 May 2016 02:35:46: 20000000 INFO @ Thu, 19 May 2016 02:35:48: 21000000 INFO @ Thu, 19 May 2016 02:35:49: 22000000 INFO @ Thu, 19 May 2016 02:35:51: 23000000 INFO @ Thu, 19 May 2016 02:35:52: 24000000 INFO @ Thu, 19 May 2016 02:35:54: 25000000 INFO @ Thu, 19 May 2016 02:35:55: 26000000 INFO @ Thu, 19 May 2016 02:35:57: 27000000 INFO @ Thu, 19 May 2016 02:35:58: 28000000 INFO @ Thu, 19 May 2016 02:36:00: 29000000 INFO @ Thu, 19 May 2016 02:36:01: 30000000 INFO @ Thu, 19 May 2016 02:36:03: 31000000 INFO @ Thu, 19 May 2016 02:36:04: 32000000 INFO @ Thu, 19 May 2016 02:36:06: 33000000 INFO @ Thu, 19 May 2016 02:36:07: 34000000 INFO @ Thu, 19 May 2016 02:36:09: 35000000 INFO @ Thu, 19 May 2016 02:36:11: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 02:36:11: #1 tag size = 76 INFO @ Thu, 19 May 2016 02:36:11: #1 total tags in treatment: 35000000 INFO @ Thu, 19 May 2016 02:36:11: #1 finished! INFO @ Thu, 19 May 2016 02:36:11: #2 Build Peak Model... INFO @ Thu, 19 May 2016 02:36:11: #2 Skipped... INFO @ Thu, 19 May 2016 02:36:11: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 02:36:11: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 02:36:11: #3 Call peaks... INFO @ Thu, 19 May 2016 02:36:11: #3 Going to call summits inside each peak ... INFO @ Thu, 19 May 2016 02:36:11: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... INFO @ Thu, 19 May 2016 02:36:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 02:37:13: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Thu, 19 May 2016 02:37:13: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg INFO @ Thu, 19 May 2016 02:37:13: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg INFO @ Thu, 19 May 2016 02:37:13: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Thu, 19 May 2016 02:37:13: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 02:46:40: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls INFO @ Thu, 19 May 2016 02:46:47: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak INFO @ Thu, 19 May 2016 02:46:53: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed INFO @ Thu, 19 May 2016 02:46:56: Done! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH INFO @ Thu, 19 May 2016 02:30:53: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff for narrow/strong regions = 1.00e-02 # pvalue cutoff for broad/weak regions = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is on INFO @ Thu, 19 May 2016 02:30:53: #1 read tag files... INFO @ Thu, 19 May 2016 02:30:53: #1 read treatment tags... INFO @ Thu, 19 May 2016 02:30:55: 1000000 INFO @ Thu, 19 May 2016 02:30:57: 2000000 INFO @ Thu, 19 May 2016 02:30:58: 3000000 INFO @ Thu, 19 May 2016 02:31:00: 4000000 INFO @ Thu, 19 May 2016 02:31:01: 5000000 INFO @ Thu, 19 May 2016 02:31:03: 6000000 INFO @ Thu, 19 May 2016 02:31:04: 7000000 INFO @ Thu, 19 May 2016 02:31:06: 8000000 INFO @ Thu, 19 May 2016 02:31:08: 9000000 INFO @ Thu, 19 May 2016 02:31:09: 10000000 INFO @ Thu, 19 May 2016 02:31:11: 11000000 INFO @ Thu, 19 May 2016 02:31:12: 12000000 INFO @ Thu, 19 May 2016 02:31:14: 13000000 INFO @ Thu, 19 May 2016 02:31:15: 14000000 INFO @ Thu, 19 May 2016 02:31:17: 15000000 INFO @ Thu, 19 May 2016 02:31:18: 16000000 INFO @ Thu, 19 May 2016 02:31:20: 17000000 INFO @ Thu, 19 May 2016 02:31:21: 18000000 INFO @ Thu, 19 May 2016 02:31:23: 19000000 INFO @ Thu, 19 May 2016 02:31:24: 20000000 INFO @ Thu, 19 May 2016 02:31:26: 21000000 INFO @ Thu, 19 May 2016 02:31:27: 22000000 INFO @ Thu, 19 May 2016 02:31:29: 23000000 INFO @ Thu, 19 May 2016 02:31:30: 24000000 INFO @ Thu, 19 May 2016 02:31:32: 25000000 INFO @ Thu, 19 May 2016 02:31:33: 26000000 INFO @ Thu, 19 May 2016 02:31:35: 27000000 INFO @ Thu, 19 May 2016 02:31:36: 28000000 INFO @ Thu, 19 May 2016 02:31:38: 29000000 INFO @ Thu, 19 May 2016 02:31:39: 30000000 INFO @ Thu, 19 May 2016 02:31:41: 31000000 INFO @ Thu, 19 May 2016 02:31:42: 32000000 INFO @ Thu, 19 May 2016 02:31:44: 33000000 INFO @ Thu, 19 May 2016 02:31:45: 34000000 INFO @ Thu, 19 May 2016 02:31:47: 35000000 INFO @ Thu, 19 May 2016 02:31:49: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 02:31:49: #1 tag size = 76 INFO @ Thu, 19 May 2016 02:31:49: #1 total tags in treatment: 35000000 INFO @ Thu, 19 May 2016 02:31:49: #1 finished! INFO @ Thu, 19 May 2016 02:31:49: #2 Build Peak Model... INFO @ Thu, 19 May 2016 02:31:49: #2 Skipped... INFO @ Thu, 19 May 2016 02:31:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 02:31:49: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 02:31:49: #3 Call peaks... INFO @ Thu, 19 May 2016 02:31:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... INFO @ Thu, 19 May 2016 02:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 02:32:51: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 02:34:23: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls INFO @ Thu, 19 May 2016 02:34:27: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak INFO @ Thu, 19 May 2016 02:34:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak INFO @ Thu, 19 May 2016 02:34:32: Done! INFO @ Thu, 19 May 2016 02:34:44: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-02 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Searching for subpeak summits is on # MACS will save fragment pileup signal per million reads INFO @ Thu, 19 May 2016 02:34:44: #1 read tag files... INFO @ Thu, 19 May 2016 02:34:44: #1 read treatment tags... INFO @ Thu, 19 May 2016 02:34:45: 1000000 INFO @ Thu, 19 May 2016 02:34:47: 2000000 INFO @ Thu, 19 May 2016 02:34:48: 3000000 INFO @ Thu, 19 May 2016 02:34:50: 4000000 INFO @ Thu, 19 May 2016 02:34:51: 5000000 INFO @ Thu, 19 May 2016 02:34:53: 6000000 INFO @ Thu, 19 May 2016 02:34:54: 7000000 INFO @ Thu, 19 May 2016 02:34:56: 8000000 INFO @ Thu, 19 May 2016 02:34:57: 9000000 INFO @ Thu, 19 May 2016 02:34:59: 10000000 INFO @ Thu, 19 May 2016 02:35:00: 11000000 INFO @ Thu, 19 May 2016 02:35:02: 12000000 INFO @ Thu, 19 May 2016 02:35:03: 13000000 INFO @ Thu, 19 May 2016 02:35:05: 14000000 INFO @ Thu, 19 May 2016 02:35:06: 15000000 INFO @ Thu, 19 May 2016 02:35:08: 16000000 INFO @ Thu, 19 May 2016 02:35:09: 17000000 INFO @ Thu, 19 May 2016 02:35:11: 18000000 INFO @ Thu, 19 May 2016 02:35:12: 19000000 INFO @ Thu, 19 May 2016 02:35:14: 20000000 INFO @ Thu, 19 May 2016 02:35:15: 21000000 INFO @ Thu, 19 May 2016 02:35:17: 22000000 INFO @ Thu, 19 May 2016 02:35:18: 23000000 INFO @ Thu, 19 May 2016 02:35:20: 24000000 INFO @ Thu, 19 May 2016 02:35:21: 25000000 INFO @ Thu, 19 May 2016 02:35:23: 26000000 INFO @ Thu, 19 May 2016 02:35:24: 27000000 INFO @ Thu, 19 May 2016 02:35:26: 28000000 INFO @ Thu, 19 May 2016 02:35:27: 29000000 INFO @ Thu, 19 May 2016 02:35:29: 30000000 INFO @ Thu, 19 May 2016 02:35:30: 31000000 INFO @ Thu, 19 May 2016 02:35:32: 32000000 INFO @ Thu, 19 May 2016 02:35:33: 33000000 INFO @ Thu, 19 May 2016 02:35:35: 34000000 INFO @ Thu, 19 May 2016 02:35:36: 35000000 INFO @ Thu, 19 May 2016 02:35:39: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 02:35:39: #1 tag size = 76 INFO @ Thu, 19 May 2016 02:35:39: #1 total tags in treatment: 35000000 INFO @ Thu, 19 May 2016 02:35:39: #1 finished! INFO @ Thu, 19 May 2016 02:35:39: #2 Build Peak Model... INFO @ Thu, 19 May 2016 02:35:39: #2 Skipped... INFO @ Thu, 19 May 2016 02:35:39: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 02:35:39: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 02:35:39: #3 Call peaks... INFO @ Thu, 19 May 2016 02:35:39: #3 Going to call summits inside each peak ... INFO @ Thu, 19 May 2016 02:35:39: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ Thu, 19 May 2016 02:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 02:36:40: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Thu, 19 May 2016 02:36:40: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg INFO @ Thu, 19 May 2016 02:36:40: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg INFO @ Thu, 19 May 2016 02:36:40: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Thu, 19 May 2016 02:36:40: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 02:41:28: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls INFO @ Thu, 19 May 2016 02:41:30: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak INFO @ Thu, 19 May 2016 02:41:31: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed INFO @ Thu, 19 May 2016 02:41:32: Done! INFO @ Thu, 19 May 2016 02:41:35: Read and build treatment bedGraph... INFO @ Thu, 19 May 2016 02:42:48: Read and build control bedGraph... INFO @ Thu, 19 May 2016 02:43:20: Build scoreTrackII... INFO @ Thu, 19 May 2016 02:43:47: Calculate scores comparing treatment and control by 'FE'... INFO @ Thu, 19 May 2016 02:47:22: Write bedGraph of scores... INFO @ Thu, 19 May 2016 02:49:28: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'! INFO @ Thu, 19 May 2016 02:54:45: Read and build treatment bedGraph... INFO @ Thu, 19 May 2016 02:55:46: Read and build control bedGraph... INFO @ Thu, 19 May 2016 02:56:14: Build scoreTrackII... INFO @ Thu, 19 May 2016 02:56:38: Values in your input bedGraph files will be multiplied by 35.000000 ... INFO @ Thu, 19 May 2016 03:00:08: Calculate scores comparing treatment and control by 'ppois'... INFO @ Thu, 19 May 2016 03:00:32: Write bedGraph of scores... INFO @ Thu, 19 May 2016 03:02:31: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 407
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 408
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH INFO @ Thu, 19 May 2016 03:08:48: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff for narrow/strong regions = 1.00e-01 # pvalue cutoff for broad/weak regions = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is on INFO @ Thu, 19 May 2016 03:08:48: #1 read tag files... INFO @ Thu, 19 May 2016 03:08:48: #1 read treatment tags... INFO @ Thu, 19 May 2016 03:08:50: 1000000 INFO @ Thu, 19 May 2016 03:08:51: 2000000 INFO @ Thu, 19 May 2016 03:08:53: 3000000 INFO @ Thu, 19 May 2016 03:08:54: 4000000 INFO @ Thu, 19 May 2016 03:08:56: 5000000 INFO @ Thu, 19 May 2016 03:08:57: 6000000 INFO @ Thu, 19 May 2016 03:08:58: 7000000 INFO @ Thu, 19 May 2016 03:09:00: 8000000 INFO @ Thu, 19 May 2016 03:09:01: 9000000 INFO @ Thu, 19 May 2016 03:09:03: 10000000 INFO @ Thu, 19 May 2016 03:09:04: 11000000 INFO @ Thu, 19 May 2016 03:09:06: 12000000 INFO @ Thu, 19 May 2016 03:09:07: 13000000 INFO @ Thu, 19 May 2016 03:09:08: 14000000 INFO @ Thu, 19 May 2016 03:09:10: 15000000 INFO @ Thu, 19 May 2016 03:09:11: 16000000 INFO @ Thu, 19 May 2016 03:09:13: 17000000 INFO @ Thu, 19 May 2016 03:09:14: 18000000 INFO @ Thu, 19 May 2016 03:09:16: 19000000 INFO @ Thu, 19 May 2016 03:09:17: 20000000 INFO @ Thu, 19 May 2016 03:09:18: 21000000 INFO @ Thu, 19 May 2016 03:09:20: 22000000 INFO @ Thu, 19 May 2016 03:09:21: 23000000 INFO @ Thu, 19 May 2016 03:09:23: 24000000 INFO @ Thu, 19 May 2016 03:09:24: 25000000 INFO @ Thu, 19 May 2016 03:09:26: 26000000 INFO @ Thu, 19 May 2016 03:09:27: 27000000 INFO @ Thu, 19 May 2016 03:09:28: 28000000 INFO @ Thu, 19 May 2016 03:09:30: 29000000 INFO @ Thu, 19 May 2016 03:09:31: 30000000 INFO @ Thu, 19 May 2016 03:09:33: 31000000 INFO @ Thu, 19 May 2016 03:09:34: 32000000 INFO @ Thu, 19 May 2016 03:09:36: 33000000 INFO @ Thu, 19 May 2016 03:09:37: 34000000 INFO @ Thu, 19 May 2016 03:09:38: 35000000 INFO @ Thu, 19 May 2016 03:09:40: 36000000 INFO @ Thu, 19 May 2016 03:09:42: 37000000 INFO @ Thu, 19 May 2016 03:09:43: 38000000 INFO @ Thu, 19 May 2016 03:09:44: 39000000 INFO @ Thu, 19 May 2016 03:09:46: 40000000 INFO @ Thu, 19 May 2016 03:09:47: 41000000 INFO @ Thu, 19 May 2016 03:09:49: 42000000 INFO @ Thu, 19 May 2016 03:09:50: 43000000 INFO @ Thu, 19 May 2016 03:09:52: 44000000 INFO @ Thu, 19 May 2016 03:09:53: 45000000 INFO @ Thu, 19 May 2016 03:09:55: 46000000 INFO @ Thu, 19 May 2016 03:09:56: 47000000 INFO @ Thu, 19 May 2016 03:09:58: 48000000 INFO @ Thu, 19 May 2016 03:09:59: 49000000 INFO @ Thu, 19 May 2016 03:10:01: 50000000 INFO @ Thu, 19 May 2016 03:10:02: 51000000 INFO @ Thu, 19 May 2016 03:10:04: 52000000 INFO @ Thu, 19 May 2016 03:10:05: 53000000 INFO @ Thu, 19 May 2016 03:10:07: 54000000 INFO @ Thu, 19 May 2016 03:10:08: 55000000 INFO @ Thu, 19 May 2016 03:10:10: 56000000 INFO @ Thu, 19 May 2016 03:10:11: 57000000 INFO @ Thu, 19 May 2016 03:10:13: 58000000 INFO @ Thu, 19 May 2016 03:10:14: 59000000 INFO @ Thu, 19 May 2016 03:10:16: 60000000 INFO @ Thu, 19 May 2016 03:10:18: 61000000 INFO @ Thu, 19 May 2016 03:10:19: 62000000 INFO @ Thu, 19 May 2016 03:10:21: 63000000 INFO @ Thu, 19 May 2016 03:10:22: 64000000 INFO @ Thu, 19 May 2016 03:10:24: 65000000 INFO @ Thu, 19 May 2016 03:10:25: 66000000 INFO @ Thu, 19 May 2016 03:10:27: 67000000 INFO @ Thu, 19 May 2016 03:10:28: 68000000 INFO @ Thu, 19 May 2016 03:10:30: 69000000 INFO @ Thu, 19 May 2016 03:10:31: 70000000 INFO @ Thu, 19 May 2016 03:10:36: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 03:10:36: #1 tag size = 76 INFO @ Thu, 19 May 2016 03:10:36: #1 total tags in treatment: 70000000 INFO @ Thu, 19 May 2016 03:10:36: #1 finished! INFO @ Thu, 19 May 2016 03:10:36: #2 Build Peak Model... INFO @ Thu, 19 May 2016 03:10:36: #2 Skipped... INFO @ Thu, 19 May 2016 03:10:36: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 03:10:36: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 03:10:36: #3 Call peaks... INFO @ Thu, 19 May 2016 03:10:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... INFO @ Thu, 19 May 2016 03:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 03:12:35: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 03:15:49: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls INFO @ Thu, 19 May 2016 03:15:52: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak INFO @ Thu, 19 May 2016 03:15:53: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak INFO @ Thu, 19 May 2016 03:15:55: Done! INFO @ Thu, 19 May 2016 03:16:04: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Searching for subpeak summits is on # MACS will save fragment pileup signal per million reads INFO @ Thu, 19 May 2016 03:16:04: #1 read tag files... INFO @ Thu, 19 May 2016 03:16:04: #1 read treatment tags... INFO @ Thu, 19 May 2016 03:16:05: 1000000 INFO @ Thu, 19 May 2016 03:16:07: 2000000 INFO @ Thu, 19 May 2016 03:16:08: 3000000 INFO @ Thu, 19 May 2016 03:16:10: 4000000 INFO @ Thu, 19 May 2016 03:16:11: 5000000 INFO @ Thu, 19 May 2016 03:16:13: 6000000 INFO @ Thu, 19 May 2016 03:16:14: 7000000 INFO @ Thu, 19 May 2016 03:16:16: 8000000 INFO @ Thu, 19 May 2016 03:16:17: 9000000 INFO @ Thu, 19 May 2016 03:16:19: 10000000 INFO @ Thu, 19 May 2016 03:16:20: 11000000 INFO @ Thu, 19 May 2016 03:16:22: 12000000 INFO @ Thu, 19 May 2016 03:16:23: 13000000 INFO @ Thu, 19 May 2016 03:16:24: 14000000 INFO @ Thu, 19 May 2016 03:16:26: 15000000 INFO @ Thu, 19 May 2016 03:16:27: 16000000 INFO @ Thu, 19 May 2016 03:16:29: 17000000 INFO @ Thu, 19 May 2016 03:16:30: 18000000 INFO @ Thu, 19 May 2016 03:16:32: 19000000 INFO @ Thu, 19 May 2016 03:16:33: 20000000 INFO @ Thu, 19 May 2016 03:16:35: 21000000 INFO @ Thu, 19 May 2016 03:16:36: 22000000 INFO @ Thu, 19 May 2016 03:16:38: 23000000 INFO @ Thu, 19 May 2016 03:16:39: 24000000 INFO @ Thu, 19 May 2016 03:16:40: 25000000 INFO @ Thu, 19 May 2016 03:16:42: 26000000 INFO @ Thu, 19 May 2016 03:16:43: 27000000 INFO @ Thu, 19 May 2016 03:16:45: 28000000 INFO @ Thu, 19 May 2016 03:16:46: 29000000 INFO @ Thu, 19 May 2016 03:16:48: 30000000 INFO @ Thu, 19 May 2016 03:16:49: 31000000 INFO @ Thu, 19 May 2016 03:16:51: 32000000 INFO @ Thu, 19 May 2016 03:16:52: 33000000 INFO @ Thu, 19 May 2016 03:16:54: 34000000 INFO @ Thu, 19 May 2016 03:16:55: 35000000 INFO @ Thu, 19 May 2016 03:16:57: 36000000 INFO @ Thu, 19 May 2016 03:16:58: 37000000 INFO @ Thu, 19 May 2016 03:17:00: 38000000 INFO @ Thu, 19 May 2016 03:17:01: 39000000 INFO @ Thu, 19 May 2016 03:17:02: 40000000 INFO @ Thu, 19 May 2016 03:17:04: 41000000 INFO @ Thu, 19 May 2016 03:17:05: 42000000 INFO @ Thu, 19 May 2016 03:17:07: 43000000 INFO @ Thu, 19 May 2016 03:17:08: 44000000 INFO @ Thu, 19 May 2016 03:17:10: 45000000 INFO @ Thu, 19 May 2016 03:17:11: 46000000 INFO @ Thu, 19 May 2016 03:17:13: 47000000 INFO @ Thu, 19 May 2016 03:17:14: 48000000 INFO @ Thu, 19 May 2016 03:17:15: 49000000 INFO @ Thu, 19 May 2016 03:17:17: 50000000 INFO @ Thu, 19 May 2016 03:17:18: 51000000 INFO @ Thu, 19 May 2016 03:17:20: 52000000 INFO @ Thu, 19 May 2016 03:17:21: 53000000 INFO @ Thu, 19 May 2016 03:17:23: 54000000 INFO @ Thu, 19 May 2016 03:17:24: 55000000 INFO @ Thu, 19 May 2016 03:17:26: 56000000 INFO @ Thu, 19 May 2016 03:17:27: 57000000 INFO @ Thu, 19 May 2016 03:17:28: 58000000 INFO @ Thu, 19 May 2016 03:17:30: 59000000 INFO @ Thu, 19 May 2016 03:17:31: 60000000 INFO @ Thu, 19 May 2016 03:17:33: 61000000 INFO @ Thu, 19 May 2016 03:17:34: 62000000 INFO @ Thu, 19 May 2016 03:17:36: 63000000 INFO @ Thu, 19 May 2016 03:17:37: 64000000 INFO @ Thu, 19 May 2016 03:17:39: 65000000 INFO @ Thu, 19 May 2016 03:17:40: 66000000 INFO @ Thu, 19 May 2016 03:17:41: 67000000 INFO @ Thu, 19 May 2016 03:17:43: 68000000 INFO @ Thu, 19 May 2016 03:17:44: 69000000 INFO @ Thu, 19 May 2016 03:17:46: 70000000 INFO @ Thu, 19 May 2016 03:17:50: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 03:17:50: #1 tag size = 76 INFO @ Thu, 19 May 2016 03:17:50: #1 total tags in treatment: 70000000 INFO @ Thu, 19 May 2016 03:17:50: #1 finished! INFO @ Thu, 19 May 2016 03:17:50: #2 Build Peak Model... INFO @ Thu, 19 May 2016 03:17:50: #2 Skipped... INFO @ Thu, 19 May 2016 03:17:50: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 03:17:50: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 03:17:50: #3 Call peaks... INFO @ Thu, 19 May 2016 03:17:50: #3 Going to call summits inside each peak ... INFO @ Thu, 19 May 2016 03:17:50: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... INFO @ Thu, 19 May 2016 03:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 03:19:45: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Thu, 19 May 2016 03:19:45: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg INFO @ Thu, 19 May 2016 03:19:45: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg INFO @ Thu, 19 May 2016 03:19:45: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Thu, 19 May 2016 03:19:45: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 03:32:42: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls INFO @ Thu, 19 May 2016 03:32:50: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak INFO @ Thu, 19 May 2016 03:32:56: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed INFO @ Thu, 19 May 2016 03:32:59: Done! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH INFO @ Thu, 19 May 2016 03:08:48: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff for narrow/strong regions = 1.00e-02 # pvalue cutoff for broad/weak regions = 1.00e-01 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is on INFO @ Thu, 19 May 2016 03:08:48: #1 read tag files... INFO @ Thu, 19 May 2016 03:08:48: #1 read treatment tags... INFO @ Thu, 19 May 2016 03:08:50: 1000000 INFO @ Thu, 19 May 2016 03:08:51: 2000000 INFO @ Thu, 19 May 2016 03:08:53: 3000000 INFO @ Thu, 19 May 2016 03:08:54: 4000000 INFO @ Thu, 19 May 2016 03:08:56: 5000000 INFO @ Thu, 19 May 2016 03:08:57: 6000000 INFO @ Thu, 19 May 2016 03:08:59: 7000000 INFO @ Thu, 19 May 2016 03:09:00: 8000000 INFO @ Thu, 19 May 2016 03:09:01: 9000000 INFO @ Thu, 19 May 2016 03:09:03: 10000000 INFO @ Thu, 19 May 2016 03:09:04: 11000000 INFO @ Thu, 19 May 2016 03:09:06: 12000000 INFO @ Thu, 19 May 2016 03:09:07: 13000000 INFO @ Thu, 19 May 2016 03:09:09: 14000000 INFO @ Thu, 19 May 2016 03:09:10: 15000000 INFO @ Thu, 19 May 2016 03:09:12: 16000000 INFO @ Thu, 19 May 2016 03:09:13: 17000000 INFO @ Thu, 19 May 2016 03:09:15: 18000000 INFO @ Thu, 19 May 2016 03:09:16: 19000000 INFO @ Thu, 19 May 2016 03:09:17: 20000000 INFO @ Thu, 19 May 2016 03:09:19: 21000000 INFO @ Thu, 19 May 2016 03:09:20: 22000000 INFO @ Thu, 19 May 2016 03:09:22: 23000000 INFO @ Thu, 19 May 2016 03:09:23: 24000000 INFO @ Thu, 19 May 2016 03:09:25: 25000000 INFO @ Thu, 19 May 2016 03:09:26: 26000000 INFO @ Thu, 19 May 2016 03:09:28: 27000000 INFO @ Thu, 19 May 2016 03:09:29: 28000000 INFO @ Thu, 19 May 2016 03:09:31: 29000000 INFO @ Thu, 19 May 2016 03:09:32: 30000000 INFO @ Thu, 19 May 2016 03:09:33: 31000000 INFO @ Thu, 19 May 2016 03:09:35: 32000000 INFO @ Thu, 19 May 2016 03:09:36: 33000000 INFO @ Thu, 19 May 2016 03:09:38: 34000000 INFO @ Thu, 19 May 2016 03:09:39: 35000000 INFO @ Thu, 19 May 2016 03:09:41: 36000000 INFO @ Thu, 19 May 2016 03:09:43: 37000000 INFO @ Thu, 19 May 2016 03:09:44: 38000000 INFO @ Thu, 19 May 2016 03:09:46: 39000000 INFO @ Thu, 19 May 2016 03:09:47: 40000000 INFO @ Thu, 19 May 2016 03:09:49: 41000000 INFO @ Thu, 19 May 2016 03:09:50: 42000000 INFO @ Thu, 19 May 2016 03:09:52: 43000000 INFO @ Thu, 19 May 2016 03:09:53: 44000000 INFO @ Thu, 19 May 2016 03:09:55: 45000000 INFO @ Thu, 19 May 2016 03:09:56: 46000000 INFO @ Thu, 19 May 2016 03:09:58: 47000000 INFO @ Thu, 19 May 2016 03:09:59: 48000000 INFO @ Thu, 19 May 2016 03:10:01: 49000000 INFO @ Thu, 19 May 2016 03:10:02: 50000000 INFO @ Thu, 19 May 2016 03:10:04: 51000000 INFO @ Thu, 19 May 2016 03:10:05: 52000000 INFO @ Thu, 19 May 2016 03:10:07: 53000000 INFO @ Thu, 19 May 2016 03:10:08: 54000000 INFO @ Thu, 19 May 2016 03:10:10: 55000000 INFO @ Thu, 19 May 2016 03:10:12: 56000000 INFO @ Thu, 19 May 2016 03:10:13: 57000000 INFO @ Thu, 19 May 2016 03:10:15: 58000000 INFO @ Thu, 19 May 2016 03:10:16: 59000000 INFO @ Thu, 19 May 2016 03:10:18: 60000000 INFO @ Thu, 19 May 2016 03:10:19: 61000000 INFO @ Thu, 19 May 2016 03:10:21: 62000000 INFO @ Thu, 19 May 2016 03:10:22: 63000000 INFO @ Thu, 19 May 2016 03:10:24: 64000000 INFO @ Thu, 19 May 2016 03:10:25: 65000000 INFO @ Thu, 19 May 2016 03:10:27: 66000000 INFO @ Thu, 19 May 2016 03:10:28: 67000000 INFO @ Thu, 19 May 2016 03:10:30: 68000000 INFO @ Thu, 19 May 2016 03:10:32: 69000000 INFO @ Thu, 19 May 2016 03:10:33: 70000000 INFO @ Thu, 19 May 2016 03:10:38: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 03:10:38: #1 tag size = 76 INFO @ Thu, 19 May 2016 03:10:38: #1 total tags in treatment: 70000000 INFO @ Thu, 19 May 2016 03:10:38: #1 finished! INFO @ Thu, 19 May 2016 03:10:38: #2 Build Peak Model... INFO @ Thu, 19 May 2016 03:10:38: #2 Skipped... INFO @ Thu, 19 May 2016 03:10:38: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 03:10:38: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 03:10:38: #3 Call peaks... INFO @ Thu, 19 May 2016 03:10:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... INFO @ Thu, 19 May 2016 03:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 03:12:43: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 03:15:26: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls INFO @ Thu, 19 May 2016 03:15:29: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak INFO @ Thu, 19 May 2016 03:15:31: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak INFO @ Thu, 19 May 2016 03:15:33: Done! INFO @ Thu, 19 May 2016 03:15:42: # Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf # format = BED # ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-02 # qvalue will not be calculated and reported as -1 in the final output. # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Searching for subpeak summits is on # MACS will save fragment pileup signal per million reads INFO @ Thu, 19 May 2016 03:15:42: #1 read tag files... INFO @ Thu, 19 May 2016 03:15:42: #1 read treatment tags... INFO @ Thu, 19 May 2016 03:15:44: 1000000 INFO @ Thu, 19 May 2016 03:15:45: 2000000 INFO @ Thu, 19 May 2016 03:15:47: 3000000 INFO @ Thu, 19 May 2016 03:15:48: 4000000 INFO @ Thu, 19 May 2016 03:15:50: 5000000 INFO @ Thu, 19 May 2016 03:15:52: 6000000 INFO @ Thu, 19 May 2016 03:15:53: 7000000 INFO @ Thu, 19 May 2016 03:15:55: 8000000 INFO @ Thu, 19 May 2016 03:15:56: 9000000 INFO @ Thu, 19 May 2016 03:15:58: 10000000 INFO @ Thu, 19 May 2016 03:16:00: 11000000 INFO @ Thu, 19 May 2016 03:16:01: 12000000 INFO @ Thu, 19 May 2016 03:16:03: 13000000 INFO @ Thu, 19 May 2016 03:16:04: 14000000 INFO @ Thu, 19 May 2016 03:16:06: 15000000 INFO @ Thu, 19 May 2016 03:16:07: 16000000 INFO @ Thu, 19 May 2016 03:16:09: 17000000 INFO @ Thu, 19 May 2016 03:16:11: 18000000 INFO @ Thu, 19 May 2016 03:16:12: 19000000 INFO @ Thu, 19 May 2016 03:16:14: 20000000 INFO @ Thu, 19 May 2016 03:16:15: 21000000 INFO @ Thu, 19 May 2016 03:16:17: 22000000 INFO @ Thu, 19 May 2016 03:16:19: 23000000 INFO @ Thu, 19 May 2016 03:16:20: 24000000 INFO @ Thu, 19 May 2016 03:16:22: 25000000 INFO @ Thu, 19 May 2016 03:16:23: 26000000 INFO @ Thu, 19 May 2016 03:16:25: 27000000 INFO @ Thu, 19 May 2016 03:16:26: 28000000 INFO @ Thu, 19 May 2016 03:16:28: 29000000 INFO @ Thu, 19 May 2016 03:16:30: 30000000 INFO @ Thu, 19 May 2016 03:16:31: 31000000 INFO @ Thu, 19 May 2016 03:16:33: 32000000 INFO @ Thu, 19 May 2016 03:16:34: 33000000 INFO @ Thu, 19 May 2016 03:16:36: 34000000 INFO @ Thu, 19 May 2016 03:16:38: 35000000 INFO @ Thu, 19 May 2016 03:16:39: 36000000 INFO @ Thu, 19 May 2016 03:16:41: 37000000 INFO @ Thu, 19 May 2016 03:16:42: 38000000 INFO @ Thu, 19 May 2016 03:16:44: 39000000 INFO @ Thu, 19 May 2016 03:16:45: 40000000 INFO @ Thu, 19 May 2016 03:16:47: 41000000 INFO @ Thu, 19 May 2016 03:16:49: 42000000 INFO @ Thu, 19 May 2016 03:16:50: 43000000 INFO @ Thu, 19 May 2016 03:16:52: 44000000 INFO @ Thu, 19 May 2016 03:16:53: 45000000 INFO @ Thu, 19 May 2016 03:16:55: 46000000 INFO @ Thu, 19 May 2016 03:16:57: 47000000 INFO @ Thu, 19 May 2016 03:16:58: 48000000 INFO @ Thu, 19 May 2016 03:17:00: 49000000 INFO @ Thu, 19 May 2016 03:17:01: 50000000 INFO @ Thu, 19 May 2016 03:17:03: 51000000 INFO @ Thu, 19 May 2016 03:17:04: 52000000 INFO @ Thu, 19 May 2016 03:17:06: 53000000 INFO @ Thu, 19 May 2016 03:17:08: 54000000 INFO @ Thu, 19 May 2016 03:17:09: 55000000 INFO @ Thu, 19 May 2016 03:17:11: 56000000 INFO @ Thu, 19 May 2016 03:17:12: 57000000 INFO @ Thu, 19 May 2016 03:17:14: 58000000 INFO @ Thu, 19 May 2016 03:17:15: 59000000 INFO @ Thu, 19 May 2016 03:17:17: 60000000 INFO @ Thu, 19 May 2016 03:17:19: 61000000 INFO @ Thu, 19 May 2016 03:17:20: 62000000 INFO @ Thu, 19 May 2016 03:17:22: 63000000 INFO @ Thu, 19 May 2016 03:17:23: 64000000 INFO @ Thu, 19 May 2016 03:17:25: 65000000 INFO @ Thu, 19 May 2016 03:17:27: 66000000 INFO @ Thu, 19 May 2016 03:17:28: 67000000 INFO @ Thu, 19 May 2016 03:17:30: 68000000 INFO @ Thu, 19 May 2016 03:17:31: 69000000 INFO @ Thu, 19 May 2016 03:17:33: 70000000 INFO @ Thu, 19 May 2016 03:17:38: #1 tag size is determined as 76 bps INFO @ Thu, 19 May 2016 03:17:38: #1 tag size = 76 INFO @ Thu, 19 May 2016 03:17:38: #1 total tags in treatment: 70000000 INFO @ Thu, 19 May 2016 03:17:38: #1 finished! INFO @ Thu, 19 May 2016 03:17:38: #2 Build Peak Model... INFO @ Thu, 19 May 2016 03:17:38: #2 Skipped... INFO @ Thu, 19 May 2016 03:17:38: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Thu, 19 May 2016 03:17:38: #2 Use 150 as fragment length INFO @ Thu, 19 May 2016 03:17:38: #3 Call peaks... INFO @ Thu, 19 May 2016 03:17:38: #3 Going to call summits inside each peak ... INFO @ Thu, 19 May 2016 03:17:38: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ Thu, 19 May 2016 03:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 19 May 2016 03:19:42: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Thu, 19 May 2016 03:19:42: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg INFO @ Thu, 19 May 2016 03:19:42: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg INFO @ Thu, 19 May 2016 03:19:42: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Thu, 19 May 2016 03:19:42: #3 Call peaks for each chromosome... INFO @ Thu, 19 May 2016 03:28:44: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls INFO @ Thu, 19 May 2016 03:28:46: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak INFO @ Thu, 19 May 2016 03:28:47: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed INFO @ Thu, 19 May 2016 03:28:48: Done! INFO @ Thu, 19 May 2016 03:28:52: Read and build treatment bedGraph... INFO @ Thu, 19 May 2016 03:31:07: Read and build control bedGraph... INFO @ Thu, 19 May 2016 03:32:07: Build scoreTrackII... INFO @ Thu, 19 May 2016 03:32:56: Calculate scores comparing treatment and control by 'FE'... INFO @ Thu, 19 May 2016 03:39:24: Write bedGraph of scores... INFO @ Thu, 19 May 2016 03:43:25: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'! INFO @ Thu, 19 May 2016 03:53:37: Read and build treatment bedGraph... INFO @ Thu, 19 May 2016 03:55:48: Read and build control bedGraph... INFO @ Thu, 19 May 2016 03:56:47: Build scoreTrackII... INFO @ Thu, 19 May 2016 03:57:36: Values in your input bedGraph files will be multiplied by 70.000000 ... INFO @ Thu, 19 May 2016 04:03:42: Calculate scores comparing treatment and control by 'ppois'... INFO @ Thu, 19 May 2016 04:04:27: Write bedGraph of scores... INFO @ Thu, 19 May 2016 04:07:15: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 138
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 141
intersectBed -wo -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | intersectBed -wo -a stdin -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz
# SYS command. line 144
echo
# SYS command. line 147
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz | sort | uniq | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz
# SYS command. line 149
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.narrowPeak.gz
--------------------Stdout-------------------- --------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 138
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 141
intersectBed -wo -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed -wo -a stdin -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz | awk 'BEGIN{FS=" ";OFS=" "} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz
# SYS command. line 144
echo
# SYS command. line 147
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz | sort | uniq | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.gz
# SYS command. line 149
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.PooledInReps.gappedPeak.gz
--------------------Stdout-------------------- --------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 74
if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 76
idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
--plot --use-best-multisummit-IDR
# SYS command. line 80
idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 83
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz
# SYS command. line 86
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz
# SYS command. line 87
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.12-col.bed.gz
# SYS command. line 89
bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
# SYS command. line 90
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS=" "} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
# SYS command. line 91
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS=" "} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz
# SYS command. line 93
gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt
# SYS command. line 94
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH Initial parameter values: [0.10 1.00 0.20 0.50] Final parameter values: [1.74 0.73 0.76 0.28] Number of reported peaks - 221438/221438 (100.0%) Number of peaks passing IDR cutoff of 0.1 - 83588/221438 (37.7%) | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 416 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz # SYS command. line 417 while [ ! -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 416 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz # SYS command. line 417 while [ ! -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 416 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz # SYS command. line 417 while [ ! -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done | ||||||||||||||||||||||||||||||||||||||||
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| # SYS command. line 416 cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.12-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz # SYS command. line 417 while [ ! -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 212
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 214
echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/IDR_final.qc
# SYS command. line 215
echo -e "83545\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/IDR_final.qc
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 300 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 125 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 848
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 852
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 854
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2
# SYS command. line 856
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2 \
--outprefix ATAC22-trimmed-pair1.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
--naive_overlap_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stdout--------------------
Run time: 2:51:44
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-19 05:09:22 ProcessExecutor Warning messages:
ERROR 2016-05-19 05:09:22 ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-19 05:09:22 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-19 05:09:22 ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-19 05:09:22 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 124 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
sorted_results = merged.sort('corr', ascending=True)
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# SYS command. line 848
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 852
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 854
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1
# SYS command. line 856
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1 \
--outprefix ATAC21-trimmed-pair1.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
--naive_overlap_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stdout--------------------
Default case invoked for:
opcode = 153, "LoopLimit"
Run time: 5:43:26
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-19 06:07:16 ProcessExecutor Warning message:
ERROR 2016-05-19 06:07:16 ProcessExecutor In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-19 06:07:16 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 298 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Could not delete file /tmp/pangwei/sortingcollection.5929993093188730966.tmp
Could not delete file /tmp/pangwei/sortingcollection.4411064961904894144.tmp
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/pangwei/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
sorted_results = merged.sort('corr', ascending=True)
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# SYS command. line 419
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 420
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp
# SYS command. line 422
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.hammock
# SYS command. line 423
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 419
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 420
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp
# SYS command. line 422
/users/pangwei/bds_atac/utils/gappedpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.hammock
# SYS command. line 423
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 419
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 420
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.tmp
# SYS command. line 422
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.hammock
# SYS command. line 423
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.12-col.bed.tmp
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 419
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 420
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
# SYS command. line 422
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock
# SYS command. line 423
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 419
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 420
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
# SYS command. line 422
/users/pangwei/bds_atac/utils/narrowpeak.py /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.hammock
# SYS command. line 423
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.tmp
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 92
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 93
dot -Tsvg /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/report/workflow.dot > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/report/workflow.svg
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 383
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 384
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 383
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 384
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.png \
-r144 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22/qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
--------------------Stderr-------------------- discarding /users/pangwei/anaconda3/bin from PATH prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21 |
| string | _ZSH_TMUX_FIXED_CONFIG | /users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf |
| bool | allowEmpty | false |
| string[] | args | [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC21+22, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC21/ATAC21-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC22/ATAC22-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19] |
| string | C_INCLUDE_PATH | /software/samtools/samtools-1.2/include/htslib |
| bool | canFail | false |
| int | cpus | 1 |
| int | cpusLocal | 48 |
| int | day | 86400 |
| real | E | 2.718281828459045 |
| int | G | 1073741824 |
| string | HOME | /users/pangwei/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | LANG | en_US.UTF-8 |
| string | LC_CTYPE | en_US.UTF-8 |
| string | LD_LIBRARY_PATH | /software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/ |
| string | LESS | -R |
| string | LOADEDMODULES | modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21 |
| string | LOGNAME | pangwei |
| string | LSCOLORS | Gxfxcxdxbxegedabagacad |
| int | M | 1048576 |
| string | /var/mail/pangwei | |
| string | MANPATH | /software/samtools/samtools-1.2/share/man:/usr/share/man |
| 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 | node | |
| int | P | 1125899906842624 |
| string | PAGER | less |
| string | PATH | /software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata |
| string | programName | atac.bds |
| string | programPath | /users/pangwei/bds_atac/atac.bds |
| string | PWD | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata |
| string | PYTHONPATH | /home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells: |
| string | queue | |
| int | retry | 0 |
| string | SAMTOOLS_HOME | /software/samtools/samtools-1.2/bin |
| string | SHELL | /usr/bin/zsh |
| string | SHLVL | 3 |
| string | SSH_AUTH_SOCK | /tmp/ssh-5gr8qSU2WF/agent.74700 |
| string | SSH_CLIENT | 171.65.76.244 36245 22 |
| string | SSH_CONNECTION | 171.65.76.244 49273 171.65.76.236 22 |
| string | SSH_TTY | /dev/pts/0 |
| string | system | local |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | THEANO_FLAGS | device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn |
| int | timeout | -1 |
| string | TMUX | /tmp/tmux-1077/default,106699,3 |
| string | TMUX_PANE | %3 |
| string | USER | pangwei |
| string | UTIL_SCRIPTS_DIR | /users/pangwei/av_scripts |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WWW | /srv/www/kundaje/pangwei |
| string | XDG_RUNTIME_DIR | /run/user/1077 |
| string | XDG_SESSION_ID | 1907 |
| string | ZSH | /users/pangwei//.oh-my-zsh |
| string | ZSH_TMUX_TERM | screen |