| Script file | /srv/scratch/annashch/bds_atac/atac.bds |
|---|---|
| Program ID | atac.bds.20160516_204447_714 |
| Start time | 2016-05-16 20:44:47 |
| Run time | 1 day 00:25:57.334 |
| Tasks executed | 26 |
| Tasks failed | 1 |
| Tasks failed names | macs2_atac rep1 |
| Arguments* | [-multimapping, 4, -out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq] |
| System* | local |
| Cpus* | 1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_20 | thread_Root | atac.bds.20160516_204447_714_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_131.id_6 atac.bds.20160516_204447_714_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_8 atac.bds.20160516_204447_714_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_321.id_10 atac.bds.20160516_204447_714_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_425.id_11 atac.bds.20160516_204447_714_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_465.id_12 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.spr_PE_rep1.line_248.id_13 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_14 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_15 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.shift_tag_rep1.line_140.id_16 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_17 atac.bds.20160516_204447_714_parallel_20/task.postalign_bed.xcor_rep1.line_165.id_18 atac.bds.20160516_204447_714_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_192.id_19 atac.bds.20160516_204447_714_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_192.id_20 atac.bds.20160516_204447_714_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_21 atac.bds.20160516_204447_714_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_192.id_22 |
| thread_21 | thread_Root | atac.bds.20160516_204447_714_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_131.id_7 atac.bds.20160516_204447_714_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9 atac.bds.20160516_204447_714_parallel_21/task.postalign_bam.nmsrt_bam_rep2.line_321.id_23 atac.bds.20160516_204447_714_parallel_21/task.postalign_bam.bam_to_bedpe_rep2.line_425.id_24 atac.bds.20160516_204447_714_parallel_21/task.postalign_bam.bedpe_to_tag_rep2.line_465.id_25 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.spr_PE_rep2.line_248.id_26 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_27 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_28 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.shift_tag_rep2.line_140.id_29 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_30 atac.bds.20160516_204447_714_parallel_21/task.postalign_bed.xcor_rep2.line_165.id_31 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 133
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 135
bowtie2 -k 4 -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized \
-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log | \
sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 133
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 135
bowtie2 -k 4 -X2000 --mm --threads 2 -x /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized \
-1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz -2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz 2>/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log | \
sambamba view -t 2 -S --format=bam /dev/stdin | sambamba sort /dev/stdin -t 2 -o /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
samtools view -F 524 -f 2 -u /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi
# SYS command. line 229
samtools view -h /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi.bam | $(which assign_multimappers.py) -k 4 --paired-end | samtools view -bS - > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam
# SYS command. line 230
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.multi.bam
# SYS command. line 237
samtools fixmate -r /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 77 files... [bam_sort_core] merging from 42 files... Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Tue May 17 10:20:03 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.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 [Tue May 17 10:20:03 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-05-17 10:20:03 MarkDuplicates Start of doWork freeMemory: 254890632; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-05-17 10:20:03 MarkDuplicates Reading input file and constructing read end information. INFO 2016-05-17 10:20:03 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-05-17 10:20:13 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr10:124,042,026 INFO 2016-05-17 10:20:13 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-05-17 10:20:22 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 9s. Last read position: chr11:115,787,636 INFO 2016-05-17 10:20:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:20:37 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 14s. Last read position: chr12:94,922,386 INFO 2016-05-17 10:20:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:20:46 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 8s. Last read position: chr14:24,583,815 INFO 2016-05-17 10:20:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:20:56 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 9s. Last read position: chr15:66,232,207 INFO 2016-05-17 10:20:56 MarkDuplicates Tracking 36 as yet unmatched pairs. 36 records in RAM. INFO 2016-05-17 10:21:02 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 6s. Last read position: chr17:8,090,517 INFO 2016-05-17 10:21:02 MarkDuplicates Tracking 30 as yet unmatched pairs. 30 records in RAM. INFO 2016-05-17 10:21:12 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 10s. Last read position: chr18:46,332,151 INFO 2016-05-17 10:21:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:21:18 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 6s. Last read position: chr1:566,085 INFO 2016-05-17 10:21:18 MarkDuplicates Tracking 4112 as yet unmatched pairs. 4112 records in RAM. INFO 2016-05-17 10:21:29 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 10s. Last read position: chr1:48,109,971 INFO 2016-05-17 10:21:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:21:35 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 6s. Last read position: chr1:182,410,164 INFO 2016-05-17 10:21:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:21:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 7s. Last read position: chr20:47,617,384 INFO 2016-05-17 10:21:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:21:51 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 8s. Last read position: chr2:43,037,759 INFO 2016-05-17 10:21:51 MarkDuplicates Tracking 40 as yet unmatched pairs. 40 records in RAM. INFO 2016-05-17 10:21:56 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 5s. Last read position: chr2:180,872,081 INFO 2016-05-17 10:21:56 MarkDuplicates Tracking 22 as yet unmatched pairs. 22 records in RAM. INFO 2016-05-17 10:22:08 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 11s. Last read position: chr3:49,131,737 INFO 2016-05-17 10:22:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:22:29 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 21s. Last read position: chr3:180,683,466 INFO 2016-05-17 10:22:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:22:36 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 7s. Last read position: chr4:138,291,665 INFO 2016-05-17 10:22:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:22:44 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 7s. Last read position: chr5:93,954,094 INFO 2016-05-17 10:22:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:22:52 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 8s. Last read position: chr6:16,215,842 INFO 2016-05-17 10:22:52 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-05-17 10:22:58 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 5s. Last read position: chr6:147,523,645 INFO 2016-05-17 10:22:58 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 10:23:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 4s. Last read position: chr7:113,883,451 INFO 2016-05-17 10:23:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:23:09 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 6s. Last read position: chr8:98,285,211 INFO 2016-05-17 10:23:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:23:14 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 4s. Last read position: chr9:110,073,218 INFO 2016-05-17 10:23:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:23:19 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 4s. Last read position: chrM:1,079 INFO 2016-05-17 10:23:19 MarkDuplicates Tracking 11558 as yet unmatched pairs. 11558 records in RAM. INFO 2016-05-17 10:23:26 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 7s. Last read position: chrM:3,082 INFO 2016-05-17 10:23:26 MarkDuplicates Tracking 46448 as yet unmatched pairs. 46448 records in RAM. INFO 2016-05-17 10:23:30 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 4s. Last read position: chrM:3,909 INFO 2016-05-17 10:23:30 MarkDuplicates Tracking 33920 as yet unmatched pairs. 33920 records in RAM. INFO 2016-05-17 10:23:34 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 4s. Last read position: chrM:4,982 INFO 2016-05-17 10:23:34 MarkDuplicates Tracking 39096 as yet unmatched pairs. 39096 records in RAM. INFO 2016-05-17 10:23:42 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 7s. Last read position: chrM:6,229 INFO 2016-05-17 10:23:42 MarkDuplicates Tracking 22334 as yet unmatched pairs. 22334 records in RAM. INFO 2016-05-17 10:23:46 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 3s. Last read position: chrM:7,469 INFO 2016-05-17 10:23:46 MarkDuplicates Tracking 34956 as yet unmatched pairs. 34956 records in RAM. INFO 2016-05-17 10:23:50 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 4s. Last read position: chrM:8,407 INFO 2016-05-17 10:23:50 MarkDuplicates Tracking 19166 as yet unmatched pairs. 19166 records in RAM. INFO 2016-05-17 10:24:06 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 16s. Last read position: chrM:9,298 INFO 2016-05-17 10:24:06 MarkDuplicates Tracking 29322 as yet unmatched pairs. 29322 records in RAM. INFO 2016-05-17 10:24:10 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 4s. Last read position: chrM:10,285 INFO 2016-05-17 10:24:10 MarkDuplicates Tracking 39766 as yet unmatched pairs. 39766 records in RAM. INFO 2016-05-17 10:24:15 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 4s. Last read position: chrM:11,221 INFO 2016-05-17 10:24:15 MarkDuplicates Tracking 32074 as yet unmatched pairs. 32074 records in RAM. INFO 2016-05-17 10:24:20 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 5s. Last read position: chrM:11,970 INFO 2016-05-17 10:24:20 MarkDuplicates Tracking 26450 as yet unmatched pairs. 26450 records in RAM. INFO 2016-05-17 10:24:24 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 4s. Last read position: chrM:12,866 INFO 2016-05-17 10:24:24 MarkDuplicates Tracking 35148 as yet unmatched pairs. 35148 records in RAM. INFO 2016-05-17 10:24:29 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 4s. Last read position: chrM:13,904 INFO 2016-05-17 10:24:29 MarkDuplicates Tracking 26334 as yet unmatched pairs. 26334 records in RAM. INFO 2016-05-17 10:24:33 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 4s. Last read position: chrM:14,996 INFO 2016-05-17 10:24:33 MarkDuplicates Tracking 31746 as yet unmatched pairs. 31746 records in RAM. INFO 2016-05-17 10:24:38 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 5s. Last read position: chrM:15,720 INFO 2016-05-17 10:24:38 MarkDuplicates Tracking 32360 as yet unmatched pairs. 32360 records in RAM. INFO 2016-05-17 10:24:43 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 4s. Last read position: chrX:31,070,729 INFO 2016-05-17 10:24:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:24:47 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 4s. Last read position: mm9_chr10:50,100,656 INFO 2016-05-17 10:24:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:24:51 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 4s. Last read position: mm9_chr10:118,477,431 INFO 2016-05-17 10:24:51 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 10:24:56 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 4s. Last read position: mm9_chr11:51,451,442 INFO 2016-05-17 10:24:56 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-05-17 10:25:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 7s. Last read position: mm9_chr11:98,609,648 INFO 2016-05-17 10:25:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:25:08 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 4s. Last read position: mm9_chr12:52,356,306 INFO 2016-05-17 10:25:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:25:13 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 4s. Last read position: mm9_chr12:119,715,955 INFO 2016-05-17 10:25:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:25:21 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 8s. Last read position: mm9_chr13:68,699,864 INFO 2016-05-17 10:25:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:25:26 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 4s. Last read position: mm9_chr14:25,006,790 INFO 2016-05-17 10:25:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:25:31 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 4s. Last read position: mm9_chr14:88,142,638 INFO 2016-05-17 10:25:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:25:37 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 6s. Last read position: mm9_chr15:36,992,534 INFO 2016-05-17 10:25:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:25:42 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 4s. Last read position: mm9_chr15:99,545,487 INFO 2016-05-17 10:25:42 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-05-17 10:25:46 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 4s. Last read position: mm9_chr16:58,473,364 INFO 2016-05-17 10:25:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:25:51 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 4s. Last read position: mm9_chr17:32,404,718 INFO 2016-05-17 10:25:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:25:55 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 4s. Last read position: mm9_chr17_random:51,081 INFO 2016-05-17 10:25:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:26:02 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 7s. Last read position: mm9_chr18:67,940,591 INFO 2016-05-17 10:26:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:26:06 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 4s. Last read position: mm9_chr19:32,419,040 INFO 2016-05-17 10:26:06 MarkDuplicates Tracking 18 as yet unmatched pairs. 18 records in RAM. INFO 2016-05-17 10:26:11 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:24,618,743 INFO 2016-05-17 10:26:11 MarkDuplicates Tracking 22752 as yet unmatched pairs. 22752 records in RAM. INFO 2016-05-17 10:26:15 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:24,619,844 INFO 2016-05-17 10:26:15 MarkDuplicates Tracking 37104 as yet unmatched pairs. 37104 records in RAM. INFO 2016-05-17 10:26:19 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:24,620,869 INFO 2016-05-17 10:26:19 MarkDuplicates Tracking 36180 as yet unmatched pairs. 36180 records in RAM. INFO 2016-05-17 10:26:27 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 7s. Last read position: mm9_chr1:24,622,109 INFO 2016-05-17 10:26:27 MarkDuplicates Tracking 25186 as yet unmatched pairs. 25186 records in RAM. INFO 2016-05-17 10:26:41 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 14s. Last read position: mm9_chr1:62,019,086 INFO 2016-05-17 10:26:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:26:45 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:136,858,855 INFO 2016-05-17 10:26:45 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 10:26:50 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:195,643,737 INFO 2016-05-17 10:26:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:26:55 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 4s. Last read position: mm9_chr2:42,078,757 INFO 2016-05-17 10:26:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:26:59 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 4s. Last read position: mm9_chr2:112,387,350 INFO 2016-05-17 10:26:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:27:05 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 6s. Last read position: mm9_chr2:166,735,708 INFO 2016-05-17 10:27:05 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 10:27:10 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 4s. Last read position: mm9_chr3:68,817,623 INFO 2016-05-17 10:27:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 10:27:14 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 4s. Last read position: mm9_chr3:131,068,453 INFO 2016-05-17 10:27:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:27:19 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 4s. Last read position: mm9_chr4:53,053,898 INFO 2016-05-17 10:27:19 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:27:23 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 4s. Last read position: mm9_chr4:124,878,191 INFO 2016-05-17 10:27:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:27:27 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 4s. Last read position: mm9_chr5:31,189,750 INFO 2016-05-17 10:27:27 MarkDuplicates Tracking 30 as yet unmatched pairs. 30 records in RAM. INFO 2016-05-17 10:27:32 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 4s. Last read position: mm9_chr5:104,134,996 INFO 2016-05-17 10:27:32 MarkDuplicates Tracking 24 as yet unmatched pairs. 24 records in RAM. INFO 2016-05-17 10:27:39 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 7s. Last read position: mm9_chr5:152,530,729 INFO 2016-05-17 10:27:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:27:43 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 4s. Last read position: mm9_chr6:83,159,215 INFO 2016-05-17 10:27:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:27:48 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 4s. Last read position: mm9_chr6:142,421,630 INFO 2016-05-17 10:27:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 10:27:56 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 8s. Last read position: mm9_chr7:74,920,807 INFO 2016-05-17 10:27:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:28:01 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 4s. Last read position: mm9_chr7:135,115,523 INFO 2016-05-17 10:28:01 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 10:28:06 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 4s. Last read position: mm9_chr8:59,391,801 INFO 2016-05-17 10:28:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:28:10 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 4s. Last read position: mm9_chr8:121,440,964 INFO 2016-05-17 10:28:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:28:17 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 6s. Last read position: mm9_chr9:56,842,306 INFO 2016-05-17 10:28:17 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 10:28:21 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 4s. Last read position: mm9_chr9:110,863,906 INFO 2016-05-17 10:28:21 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 10:28:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:510 INFO 2016-05-17 10:28:25 MarkDuplicates Tracking 60330 as yet unmatched pairs. 60330 records in RAM. INFO 2016-05-17 10:28:29 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,199 INFO 2016-05-17 10:28:29 MarkDuplicates Tracking 43760 as yet unmatched pairs. 43760 records in RAM. INFO 2016-05-17 10:28:33 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,924 INFO 2016-05-17 10:28:33 MarkDuplicates Tracking 39184 as yet unmatched pairs. 39184 records in RAM. INFO 2016-05-17 10:28:37 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:2,721 INFO 2016-05-17 10:28:37 MarkDuplicates Tracking 40840 as yet unmatched pairs. 40840 records in RAM. INFO 2016-05-17 10:28:41 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:3,319 INFO 2016-05-17 10:28:41 MarkDuplicates Tracking 51472 as yet unmatched pairs. 51472 records in RAM. INFO 2016-05-17 10:28:45 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,913 INFO 2016-05-17 10:28:45 MarkDuplicates Tracking 44282 as yet unmatched pairs. 44282 records in RAM. INFO 2016-05-17 10:28:53 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 7s. Last read position: mm9_chrM:4,541 INFO 2016-05-17 10:28:53 MarkDuplicates Tracking 38654 as yet unmatched pairs. 38654 records in RAM. INFO 2016-05-17 10:28:57 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:5,367 INFO 2016-05-17 10:28:57 MarkDuplicates Tracking 34632 as yet unmatched pairs. 34632 records in RAM. INFO 2016-05-17 10:29:01 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:5,944 INFO 2016-05-17 10:29:01 MarkDuplicates Tracking 52744 as yet unmatched pairs. 52744 records in RAM. INFO 2016-05-17 10:29:16 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 14s. Last read position: mm9_chrM:6,688 INFO 2016-05-17 10:29:16 MarkDuplicates Tracking 33918 as yet unmatched pairs. 33918 records in RAM. INFO 2016-05-17 10:29:20 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:7,984 INFO 2016-05-17 10:29:20 MarkDuplicates Tracking 22648 as yet unmatched pairs. 22648 records in RAM. INFO 2016-05-17 10:29:24 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:9,102 INFO 2016-05-17 10:29:24 MarkDuplicates Tracking 30188 as yet unmatched pairs. 30188 records in RAM. INFO 2016-05-17 10:29:28 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:10,516 INFO 2016-05-17 10:29:28 MarkDuplicates Tracking 22806 as yet unmatched pairs. 22806 records in RAM. INFO 2016-05-17 10:29:32 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,310 INFO 2016-05-17 10:29:32 MarkDuplicates Tracking 65824 as yet unmatched pairs. 65824 records in RAM. INFO 2016-05-17 10:29:36 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:12,058 INFO 2016-05-17 10:29:36 MarkDuplicates Tracking 40160 as yet unmatched pairs. 40160 records in RAM. INFO 2016-05-17 10:29:42 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 5s. Last read position: mm9_chrM:12,635 INFO 2016-05-17 10:29:42 MarkDuplicates Tracking 49286 as yet unmatched pairs. 49286 records in RAM. INFO 2016-05-17 10:29:46 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:13,229 INFO 2016-05-17 10:29:46 MarkDuplicates Tracking 48148 as yet unmatched pairs. 48148 records in RAM. INFO 2016-05-17 10:29:49 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:13,911 INFO 2016-05-17 10:29:49 MarkDuplicates Tracking 51858 as yet unmatched pairs. 51858 records in RAM. INFO 2016-05-17 10:29:53 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:14,509 INFO 2016-05-17 10:29:53 MarkDuplicates Tracking 45788 as yet unmatched pairs. 45788 records in RAM. INFO 2016-05-17 10:29:57 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:15,075 INFO 2016-05-17 10:29:57 MarkDuplicates Tracking 55926 as yet unmatched pairs. 55926 records in RAM. INFO 2016-05-17 10:30:01 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:16,108 INFO 2016-05-17 10:30:01 MarkDuplicates Tracking 10802 as yet unmatched pairs. 10802 records in RAM. INFO 2016-05-17 10:30:06 MarkDuplicates Read 100967372 records. 0 pairs never matched. INFO 2016-05-17 10:30:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 2854052576; totalMemory: 2882011136; maxMemory: 3817865216 INFO 2016-05-17 10:30:14 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk. INFO 2016-05-17 10:30:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-05-17 10:30:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-05-17 10:31:03 MarkDuplicates Sorting list of duplicate records. INFO 2016-05-17 10:31:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 1882718088; totalMemory: 2864185344; maxMemory: 3817865216 INFO 2016-05-17 10:31:06 MarkDuplicates Marking 42877902 records as duplicates. INFO 2016-05-17 10:31:06 MarkDuplicates Found 7658471 optical duplicate clusters. INFO 2016-05-17 10:33:05 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:57s. Time for last 10,000,000: 117s. Last read position: chr1:182,410,164 INFO 2016-05-17 10:35:08 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:04:00s. Time for last 10,000,000: 122s. Last read position: chr7:113,883,451 INFO 2016-05-17 10:37:01 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:05:53s. Time for last 10,000,000: 113s. Last read position: chrM:9,298 INFO 2016-05-17 10:38:55 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:07:47s. Time for last 10,000,000: 113s. Last read position: mm9_chr10:118,477,431 INFO 2016-05-17 10:41:00 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:09:53s. Time for last 10,000,000: 125s. Last read position: mm9_chr16:58,473,364 INFO 2016-05-17 10:42:58 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:11:50s. Time for last 10,000,000: 117s. Last read position: mm9_chr1:136,858,855 INFO 2016-05-17 10:45:04 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:13:56s. Time for last 10,000,000: 125s. Last read position: mm9_chr5:104,134,996 INFO 2016-05-17 10:47:09 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:16:02s. Time for last 10,000,000: 125s. Last read position: mm9_chrM:510 INFO 2016-05-17 10:48:56 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:17:48s. Time for last 10,000,000: 106s. Last read position: mm9_chrM:7,984 INFO 2016-05-17 10:50:43 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:19:36s. Time for last 10,000,000: 107s. Last read position: mm9_chrM:16,108 INFO 2016-05-17 10:50:56 MarkDuplicates Before output close freeMemory: 2978663800; totalMemory: 3008888832; maxMemory: 3817865216 INFO 2016-05-17 10:50:56 MarkDuplicates After output close freeMemory: 2978662744; totalMemory: 3008888832; maxMemory: 3817865216 [Tue May 17 10:50:56 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.88 minutes. Runtime.totalMemory()=3008888832 [bam_sort_core] merging from 42 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
samtools view -F 524 -f 2 -u /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi
# SYS command. line 229
samtools view -h /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi.bam | $(which assign_multimappers.py) -k 4 --paired-end | samtools view -bS - > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam
# SYS command. line 230
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.multi.bam
# SYS command. line 237
samtools fixmate -r /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam.bai /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 154 files... [bam_sort_core] merging from 72 files... Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Tue May 17 17:33:30 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.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 [Tue May 17 17:33:30 PDT 2016] Executing as annashch@kali on Linux 3.19.0-25-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-05-17 17:33:30 MarkDuplicates Start of doWork freeMemory: 254890776; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-05-17 17:33:30 MarkDuplicates Reading input file and constructing read end information. INFO 2016-05-17 17:33:30 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-05-17 17:33:35 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr11:60,609,172 INFO 2016-05-17 17:33:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:33:40 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 4s. Last read position: chr12:101,852,588 INFO 2016-05-17 17:33:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:33:45 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 4s. Last read position: chr14:91,654,768 INFO 2016-05-17 17:33:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:33:50 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 5s. Last read position: chr17:6,312,803 INFO 2016-05-17 17:33:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:33:56 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 6s. Last read position: chr19:18,391,782 INFO 2016-05-17 17:33:56 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 17:34:02 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 6s. Last read position: chr1:565,632 INFO 2016-05-17 17:34:02 MarkDuplicates Tracking 50588 as yet unmatched pairs. 50588 records in RAM. INFO 2016-05-17 17:34:07 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 4s. Last read position: chr1:567,590 INFO 2016-05-17 17:34:07 MarkDuplicates Tracking 6660 as yet unmatched pairs. 6660 records in RAM. INFO 2016-05-17 17:34:12 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 5s. Last read position: chr1:569,886 INFO 2016-05-17 17:34:12 MarkDuplicates Tracking 16026 as yet unmatched pairs. 16026 records in RAM. INFO 2016-05-17 17:34:16 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 4s. Last read position: chr1:112,946,804 INFO 2016-05-17 17:34:16 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 17:34:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 5s. Last read position: chr20:51,110,997 INFO 2016-05-17 17:34:22 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 17:34:27 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 5s. Last read position: chr2:121,493,894 INFO 2016-05-17 17:34:27 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-05-17 17:34:34 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 7s. Last read position: chr3:47,554,068 INFO 2016-05-17 17:34:34 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:34:40 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 5s. Last read position: chr4:45,561,192 INFO 2016-05-17 17:34:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:34:45 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 5s. Last read position: chr5:87,988,986 INFO 2016-05-17 17:34:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:35:05 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 20s. Last read position: chr6:11,161,694 INFO 2016-05-17 17:35:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:35:09 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 4s. Last read position: chr7:40,194,472 INFO 2016-05-17 17:35:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:35:14 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 4s. Last read position: chr8:96,317,828 INFO 2016-05-17 17:35:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:35:19 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 5s. Last read position: chrM:29 INFO 2016-05-17 17:35:19 MarkDuplicates Tracking 29602 as yet unmatched pairs. 29602 records in RAM. INFO 2016-05-17 17:35:24 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 5s. Last read position: chrM:572 INFO 2016-05-17 17:35:24 MarkDuplicates Tracking 21846 as yet unmatched pairs. 21846 records in RAM. INFO 2016-05-17 17:35:31 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 6s. Last read position: chrM:1,336 INFO 2016-05-17 17:35:31 MarkDuplicates Tracking 67266 as yet unmatched pairs. 67266 records in RAM. INFO 2016-05-17 17:35:35 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 4s. Last read position: chrM:2,335 INFO 2016-05-17 17:35:35 MarkDuplicates Tracking 67724 as yet unmatched pairs. 67724 records in RAM. INFO 2016-05-17 17:35:39 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 4s. Last read position: chrM:2,851 INFO 2016-05-17 17:35:39 MarkDuplicates Tracking 69958 as yet unmatched pairs. 69958 records in RAM. INFO 2016-05-17 17:35:43 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: chrM:3,243 INFO 2016-05-17 17:35:43 MarkDuplicates Tracking 100048 as yet unmatched pairs. 100048 records in RAM. INFO 2016-05-17 17:35:47 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chrM:3,487 INFO 2016-05-17 17:35:47 MarkDuplicates Tracking 27154 as yet unmatched pairs. 27154 records in RAM. INFO 2016-05-17 17:35:51 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 4s. Last read position: chrM:3,784 INFO 2016-05-17 17:35:51 MarkDuplicates Tracking 53212 as yet unmatched pairs. 53212 records in RAM. INFO 2016-05-17 17:35:58 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 7s. Last read position: chrM:4,067 INFO 2016-05-17 17:35:58 MarkDuplicates Tracking 66852 as yet unmatched pairs. 66852 records in RAM. INFO 2016-05-17 17:36:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 4s. Last read position: chrM:4,526 INFO 2016-05-17 17:36:02 MarkDuplicates Tracking 49270 as yet unmatched pairs. 49270 records in RAM. INFO 2016-05-17 17:36:06 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 4s. Last read position: chrM:4,913 INFO 2016-05-17 17:36:06 MarkDuplicates Tracking 55228 as yet unmatched pairs. 55228 records in RAM. INFO 2016-05-17 17:36:15 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 8s. Last read position: chrM:5,309 INFO 2016-05-17 17:36:15 MarkDuplicates Tracking 38758 as yet unmatched pairs. 38758 records in RAM. INFO 2016-05-17 17:36:29 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 14s. Last read position: chrM:5,789 INFO 2016-05-17 17:36:29 MarkDuplicates Tracking 31784 as yet unmatched pairs. 31784 records in RAM. INFO 2016-05-17 17:36:33 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 4s. Last read position: chrM:6,202 INFO 2016-05-17 17:36:33 MarkDuplicates Tracking 37486 as yet unmatched pairs. 37486 records in RAM. INFO 2016-05-17 17:36:38 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 4s. Last read position: chrM:6,483 INFO 2016-05-17 17:36:38 MarkDuplicates Tracking 36094 as yet unmatched pairs. 36094 records in RAM. INFO 2016-05-17 17:36:43 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 5s. Last read position: chrM:7,010 INFO 2016-05-17 17:36:43 MarkDuplicates Tracking 38106 as yet unmatched pairs. 38106 records in RAM. INFO 2016-05-17 17:36:48 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 4s. Last read position: chrM:7,504 INFO 2016-05-17 17:36:48 MarkDuplicates Tracking 100568 as yet unmatched pairs. 100568 records in RAM. INFO 2016-05-17 17:36:54 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 6s. Last read position: chrM:7,822 INFO 2016-05-17 17:36:54 MarkDuplicates Tracking 45244 as yet unmatched pairs. 45244 records in RAM. INFO 2016-05-17 17:36:59 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 4s. Last read position: chrM:8,156 INFO 2016-05-17 17:36:59 MarkDuplicates Tracking 64112 as yet unmatched pairs. 64112 records in RAM. INFO 2016-05-17 17:37:03 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 4s. Last read position: chrM:8,583 INFO 2016-05-17 17:37:03 MarkDuplicates Tracking 33094 as yet unmatched pairs. 33094 records in RAM. INFO 2016-05-17 17:37:07 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 4s. Last read position: chrM:8,941 INFO 2016-05-17 17:37:07 MarkDuplicates Tracking 56702 as yet unmatched pairs. 56702 records in RAM. INFO 2016-05-17 17:37:12 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 4s. Last read position: chrM:9,219 INFO 2016-05-17 17:37:12 MarkDuplicates Tracking 39766 as yet unmatched pairs. 39766 records in RAM. INFO 2016-05-17 17:37:16 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 4s. Last read position: chrM:9,589 INFO 2016-05-17 17:37:16 MarkDuplicates Tracking 30698 as yet unmatched pairs. 30698 records in RAM. INFO 2016-05-17 17:37:23 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 7s. Last read position: chrM:9,868 INFO 2016-05-17 17:37:23 MarkDuplicates Tracking 87822 as yet unmatched pairs. 87822 records in RAM. INFO 2016-05-17 17:37:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 4s. Last read position: chrM:10,195 INFO 2016-05-17 17:37:27 MarkDuplicates Tracking 56334 as yet unmatched pairs. 56334 records in RAM. INFO 2016-05-17 17:37:31 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 4s. Last read position: chrM:10,462 INFO 2016-05-17 17:37:31 MarkDuplicates Tracking 86724 as yet unmatched pairs. 86724 records in RAM. INFO 2016-05-17 17:37:35 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 4s. Last read position: chrM:10,685 INFO 2016-05-17 17:37:35 MarkDuplicates Tracking 24650 as yet unmatched pairs. 24650 records in RAM. INFO 2016-05-17 17:37:44 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 8s. Last read position: chrM:11,129 INFO 2016-05-17 17:37:44 MarkDuplicates Tracking 68626 as yet unmatched pairs. 68626 records in RAM. INFO 2016-05-17 17:37:48 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 4s. Last read position: chrM:11,353 INFO 2016-05-17 17:37:48 MarkDuplicates Tracking 51424 as yet unmatched pairs. 51424 records in RAM. INFO 2016-05-17 17:37:53 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 5s. Last read position: chrM:11,616 INFO 2016-05-17 17:37:53 MarkDuplicates Tracking 37638 as yet unmatched pairs. 37638 records in RAM. INFO 2016-05-17 17:37:59 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 5s. Last read position: chrM:11,884 INFO 2016-05-17 17:37:59 MarkDuplicates Tracking 61206 as yet unmatched pairs. 61206 records in RAM. INFO 2016-05-17 17:38:06 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 7s. Last read position: chrM:12,147 INFO 2016-05-17 17:38:06 MarkDuplicates Tracking 63078 as yet unmatched pairs. 63078 records in RAM. INFO 2016-05-17 17:38:10 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 4s. Last read position: chrM:12,537 INFO 2016-05-17 17:38:10 MarkDuplicates Tracking 59870 as yet unmatched pairs. 59870 records in RAM. INFO 2016-05-17 17:38:14 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 4s. Last read position: chrM:12,795 INFO 2016-05-17 17:38:14 MarkDuplicates Tracking 44656 as yet unmatched pairs. 44656 records in RAM. INFO 2016-05-17 17:38:19 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 4s. Last read position: chrM:13,117 INFO 2016-05-17 17:38:19 MarkDuplicates Tracking 43018 as yet unmatched pairs. 43018 records in RAM. INFO 2016-05-17 17:38:23 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 4s. Last read position: chrM:13,445 INFO 2016-05-17 17:38:23 MarkDuplicates Tracking 38546 as yet unmatched pairs. 38546 records in RAM. INFO 2016-05-17 17:38:27 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 4s. Last read position: chrM:13,849 INFO 2016-05-17 17:38:27 MarkDuplicates Tracking 74746 as yet unmatched pairs. 74746 records in RAM. INFO 2016-05-17 17:38:31 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 4s. Last read position: chrM:14,149 INFO 2016-05-17 17:38:31 MarkDuplicates Tracking 53364 as yet unmatched pairs. 53364 records in RAM. INFO 2016-05-17 17:38:39 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 7s. Last read position: chrM:14,621 INFO 2016-05-17 17:38:39 MarkDuplicates Tracking 16986 as yet unmatched pairs. 16986 records in RAM. INFO 2016-05-17 17:38:44 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 4s. Last read position: chrM:15,016 INFO 2016-05-17 17:38:44 MarkDuplicates Tracking 58882 as yet unmatched pairs. 58882 records in RAM. INFO 2016-05-17 17:38:48 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 4s. Last read position: chrM:15,252 INFO 2016-05-17 17:38:48 MarkDuplicates Tracking 59190 as yet unmatched pairs. 59190 records in RAM. INFO 2016-05-17 17:39:05 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 17s. Last read position: chrM:15,511 INFO 2016-05-17 17:39:05 MarkDuplicates Tracking 39322 as yet unmatched pairs. 39322 records in RAM. INFO 2016-05-17 17:39:09 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 4s. Last read position: chrM:15,767 INFO 2016-05-17 17:39:09 MarkDuplicates Tracking 42312 as yet unmatched pairs. 42312 records in RAM. INFO 2016-05-17 17:39:13 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 4s. Last read position: chrM:16,083 INFO 2016-05-17 17:39:13 MarkDuplicates Tracking 51126 as yet unmatched pairs. 51126 records in RAM. INFO 2016-05-17 17:39:17 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 4s. Last read position: chrM:16,404 INFO 2016-05-17 17:39:17 MarkDuplicates Tracking 39502 as yet unmatched pairs. 39502 records in RAM. INFO 2016-05-17 17:39:24 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 6s. Last read position: mm9_chr10:24,315,691 INFO 2016-05-17 17:39:24 MarkDuplicates Tracking 30 as yet unmatched pairs. 30 records in RAM. INFO 2016-05-17 17:39:31 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 7s. Last read position: mm9_chr10:94,672,081 INFO 2016-05-17 17:39:31 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:39:36 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 4s. Last read position: mm9_chr11:29,147,440 INFO 2016-05-17 17:39:36 MarkDuplicates Tracking 42 as yet unmatched pairs. 42 records in RAM. INFO 2016-05-17 17:39:41 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 5s. Last read position: mm9_chr11:95,638,909 INFO 2016-05-17 17:39:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:39:46 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 5s. Last read position: mm9_chr12:58,080,039 INFO 2016-05-17 17:39:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:39:51 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 4s. Last read position: mm9_chr13:5,224,680 INFO 2016-05-17 17:39:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:39:56 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 4s. Last read position: mm9_chr13:85,266,763 INFO 2016-05-17 17:39:56 MarkDuplicates Tracking 294 as yet unmatched pairs. 294 records in RAM. INFO 2016-05-17 17:40:00 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 4s. Last read position: mm9_chr14:55,042,357 INFO 2016-05-17 17:40:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:40:05 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 4s. Last read position: mm9_chr15:25,200,459 INFO 2016-05-17 17:40:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:40:13 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 7s. Last read position: mm9_chr15:100,430,621 INFO 2016-05-17 17:40:13 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 17:40:17 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 4s. Last read position: mm9_chr16:86,143,136 INFO 2016-05-17 17:40:17 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:40:25 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 8s. Last read position: mm9_chr17:57,200,071 INFO 2016-05-17 17:40:25 MarkDuplicates Tracking 22 as yet unmatched pairs. 22 records in RAM. INFO 2016-05-17 17:40:29 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 4s. Last read position: mm9_chr18:46,901,150 INFO 2016-05-17 17:40:29 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-05-17 17:40:35 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 6s. Last read position: mm9_chr19:38,961,254 INFO 2016-05-17 17:40:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:40:41 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 6s. Last read position: mm9_chr1:24,618,562 INFO 2016-05-17 17:40:41 MarkDuplicates Tracking 43408 as yet unmatched pairs. 43408 records in RAM. INFO 2016-05-17 17:40:48 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 6s. Last read position: mm9_chr1:24,618,950 INFO 2016-05-17 17:40:48 MarkDuplicates Tracking 61590 as yet unmatched pairs. 61590 records in RAM. INFO 2016-05-17 17:40:52 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:24,619,311 INFO 2016-05-17 17:40:52 MarkDuplicates Tracking 39830 as yet unmatched pairs. 39830 records in RAM. INFO 2016-05-17 17:40:57 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:24,619,564 INFO 2016-05-17 17:40:57 MarkDuplicates Tracking 162352 as yet unmatched pairs. 162352 records in RAM. INFO 2016-05-17 17:41:03 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 6s. Last read position: mm9_chr1:24,619,881 INFO 2016-05-17 17:41:03 MarkDuplicates Tracking 63556 as yet unmatched pairs. 63556 records in RAM. INFO 2016-05-17 17:41:07 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,620,180 INFO 2016-05-17 17:41:07 MarkDuplicates Tracking 36820 as yet unmatched pairs. 36820 records in RAM. INFO 2016-05-17 17:41:10 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,620,495 INFO 2016-05-17 17:41:10 MarkDuplicates Tracking 65140 as yet unmatched pairs. 65140 records in RAM. INFO 2016-05-17 17:41:14 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,620,818 INFO 2016-05-17 17:41:14 MarkDuplicates Tracking 35064 as yet unmatched pairs. 35064 records in RAM. INFO 2016-05-17 17:41:17 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,621,171 INFO 2016-05-17 17:41:17 MarkDuplicates Tracking 31144 as yet unmatched pairs. 31144 records in RAM. INFO 2016-05-17 17:41:21 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,621,571 INFO 2016-05-17 17:41:21 MarkDuplicates Tracking 64260 as yet unmatched pairs. 64260 records in RAM. INFO 2016-05-17 17:41:25 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,621,988 INFO 2016-05-17 17:41:25 MarkDuplicates Tracking 48714 as yet unmatched pairs. 48714 records in RAM. INFO 2016-05-17 17:41:29 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 3s. Last read position: mm9_chr1:24,622,358 INFO 2016-05-17 17:41:29 MarkDuplicates Tracking 31882 as yet unmatched pairs. 31882 records in RAM. INFO 2016-05-17 17:41:42 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 13s. Last read position: mm9_chr1:24,622,907 INFO 2016-05-17 17:41:42 MarkDuplicates Tracking 11634 as yet unmatched pairs. 11634 records in RAM. INFO 2016-05-17 17:41:47 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:107,710,266 INFO 2016-05-17 17:41:47 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM. INFO 2016-05-17 17:41:52 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 4s. Last read position: mm9_chr1:182,152,842 INFO 2016-05-17 17:41:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:41:56 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 3s. Last read position: mm9_chr2:22,444,191 INFO 2016-05-17 17:41:56 MarkDuplicates Tracking 3478 as yet unmatched pairs. 3478 records in RAM. INFO 2016-05-17 17:41:59 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 3s. Last read position: mm9_chr2:29,340,691 INFO 2016-05-17 17:41:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:42:03 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 4s. Last read position: mm9_chr2:102,024,638 INFO 2016-05-17 17:42:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 17:42:08 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 4s. Last read position: mm9_chr2:164,169,400 INFO 2016-05-17 17:42:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:42:12 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 4s. Last read position: mm9_chr3:83,373,984 INFO 2016-05-17 17:42:12 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM. INFO 2016-05-17 17:42:16 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 4s. Last read position: mm9_chr3:147,011,700 INFO 2016-05-17 17:42:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:42:20 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 4s. Last read position: mm9_chr4:82,020,621 INFO 2016-05-17 17:42:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM. INFO 2016-05-17 17:42:24 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 3s. Last read position: mm9_chr4:146,649,690 INFO 2016-05-17 17:42:24 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2016-05-17 17:42:30 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 6s. Last read position: mm9_chr5:74,867,694 INFO 2016-05-17 17:42:30 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:42:34 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 4s. Last read position: mm9_chr5:141,306,473 INFO 2016-05-17 17:42:34 MarkDuplicates Tracking 58 as yet unmatched pairs. 58 records in RAM. INFO 2016-05-17 17:42:38 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 4s. Last read position: mm9_chr6:77,122,934 INFO 2016-05-17 17:42:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:42:46 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 7s. Last read position: mm9_chr6:145,921,768 INFO 2016-05-17 17:42:46 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM. INFO 2016-05-17 17:42:50 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 4s. Last read position: mm9_chr7:89,765,004 INFO 2016-05-17 17:42:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-05-17 17:42:55 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 4s. Last read position: mm9_chr8:9,811,383 INFO 2016-05-17 17:42:55 MarkDuplicates Tracking 46 as yet unmatched pairs. 46 records in RAM. INFO 2016-05-17 17:42:59 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 4s. Last read position: mm9_chr8:91,517,419 INFO 2016-05-17 17:42:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:43:03 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 4s. Last read position: mm9_chr9:38,456,884 INFO 2016-05-17 17:43:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:43:07 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 4s. Last read position: mm9_chr9:107,208,572 INFO 2016-05-17 17:43:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2016-05-17 17:43:11 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:143 INFO 2016-05-17 17:43:11 MarkDuplicates Tracking 91124 as yet unmatched pairs. 91124 records in RAM. INFO 2016-05-17 17:43:15 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:343 INFO 2016-05-17 17:43:15 MarkDuplicates Tracking 178920 as yet unmatched pairs. 178920 records in RAM. INFO 2016-05-17 17:43:22 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 6s. Last read position: mm9_chrM:597 INFO 2016-05-17 17:43:22 MarkDuplicates Tracking 39322 as yet unmatched pairs. 39322 records in RAM. INFO 2016-05-17 17:43:26 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:810 INFO 2016-05-17 17:43:26 MarkDuplicates Tracking 111996 as yet unmatched pairs. 111996 records in RAM. INFO 2016-05-17 17:43:30 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:999 INFO 2016-05-17 17:43:30 MarkDuplicates Tracking 82614 as yet unmatched pairs. 82614 records in RAM. INFO 2016-05-17 17:43:33 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,196 INFO 2016-05-17 17:43:33 MarkDuplicates Tracking 92366 as yet unmatched pairs. 92366 records in RAM. INFO 2016-05-17 17:43:37 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,436 INFO 2016-05-17 17:43:37 MarkDuplicates Tracking 151980 as yet unmatched pairs. 151980 records in RAM. INFO 2016-05-17 17:43:41 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,672 INFO 2016-05-17 17:43:41 MarkDuplicates Tracking 97038 as yet unmatched pairs. 97038 records in RAM. INFO 2016-05-17 17:43:45 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:1,899 INFO 2016-05-17 17:43:45 MarkDuplicates Tracking 86848 as yet unmatched pairs. 86848 records in RAM. INFO 2016-05-17 17:43:58 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 13s. Last read position: mm9_chrM:2,179 INFO 2016-05-17 17:43:58 MarkDuplicates Tracking 144554 as yet unmatched pairs. 144554 records in RAM. INFO 2016-05-17 17:44:02 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:2,471 INFO 2016-05-17 17:44:02 MarkDuplicates Tracking 64836 as yet unmatched pairs. 64836 records in RAM. INFO 2016-05-17 17:44:06 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:2,677 INFO 2016-05-17 17:44:06 MarkDuplicates Tracking 170274 as yet unmatched pairs. 170274 records in RAM. INFO 2016-05-17 17:44:12 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 5s. Last read position: mm9_chrM:2,858 INFO 2016-05-17 17:44:12 MarkDuplicates Tracking 121410 as yet unmatched pairs. 121410 records in RAM. INFO 2016-05-17 17:44:16 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,030 INFO 2016-05-17 17:44:16 MarkDuplicates Tracking 133364 as yet unmatched pairs. 133364 records in RAM. INFO 2016-05-17 17:44:20 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,232 INFO 2016-05-17 17:44:20 MarkDuplicates Tracking 60386 as yet unmatched pairs. 60386 records in RAM. INFO 2016-05-17 17:44:23 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,429 INFO 2016-05-17 17:44:23 MarkDuplicates Tracking 51512 as yet unmatched pairs. 51512 records in RAM. INFO 2016-05-17 17:44:27 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,588 INFO 2016-05-17 17:44:27 MarkDuplicates Tracking 103458 as yet unmatched pairs. 103458 records in RAM. INFO 2016-05-17 17:44:31 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,768 INFO 2016-05-17 17:44:31 MarkDuplicates Tracking 111898 as yet unmatched pairs. 111898 records in RAM. INFO 2016-05-17 17:44:35 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:3,953 INFO 2016-05-17 17:44:35 MarkDuplicates Tracking 66894 as yet unmatched pairs. 66894 records in RAM. INFO 2016-05-17 17:44:38 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:4,136 INFO 2016-05-17 17:44:38 MarkDuplicates Tracking 102944 as yet unmatched pairs. 102944 records in RAM. INFO 2016-05-17 17:44:42 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:4,320 INFO 2016-05-17 17:44:42 MarkDuplicates Tracking 123612 as yet unmatched pairs. 123612 records in RAM. INFO 2016-05-17 17:44:45 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:4,529 INFO 2016-05-17 17:44:45 MarkDuplicates Tracking 75514 as yet unmatched pairs. 75514 records in RAM. INFO 2016-05-17 17:44:49 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:4,704 INFO 2016-05-17 17:44:49 MarkDuplicates Tracking 153024 as yet unmatched pairs. 153024 records in RAM. INFO 2016-05-17 17:44:56 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 6s. Last read position: mm9_chrM:5,064 INFO 2016-05-17 17:44:56 MarkDuplicates Tracking 97482 as yet unmatched pairs. 97482 records in RAM. INFO 2016-05-17 17:45:04 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 7s. Last read position: mm9_chrM:5,320 INFO 2016-05-17 17:45:04 MarkDuplicates Tracking 108002 as yet unmatched pairs. 108002 records in RAM. INFO 2016-05-17 17:45:08 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:5,505 INFO 2016-05-17 17:45:08 MarkDuplicates Tracking 133118 as yet unmatched pairs. 133118 records in RAM. INFO 2016-05-17 17:45:12 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:5,740 INFO 2016-05-17 17:45:12 MarkDuplicates Tracking 92606 as yet unmatched pairs. 92606 records in RAM. INFO 2016-05-17 17:45:15 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:5,896 INFO 2016-05-17 17:45:15 MarkDuplicates Tracking 52108 as yet unmatched pairs. 52108 records in RAM. INFO 2016-05-17 17:45:19 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:6,080 INFO 2016-05-17 17:45:19 MarkDuplicates Tracking 100148 as yet unmatched pairs. 100148 records in RAM. INFO 2016-05-17 17:45:23 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:6,253 INFO 2016-05-17 17:45:23 MarkDuplicates Tracking 99748 as yet unmatched pairs. 99748 records in RAM. INFO 2016-05-17 17:45:27 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:6,477 INFO 2016-05-17 17:45:27 MarkDuplicates Tracking 27970 as yet unmatched pairs. 27970 records in RAM. INFO 2016-05-17 17:45:31 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:6,997 INFO 2016-05-17 17:45:31 MarkDuplicates Tracking 20148 as yet unmatched pairs. 20148 records in RAM. INFO 2016-05-17 17:45:35 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:7,362 INFO 2016-05-17 17:45:35 MarkDuplicates Tracking 51210 as yet unmatched pairs. 51210 records in RAM. INFO 2016-05-17 17:45:38 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:7,774 INFO 2016-05-17 17:45:38 MarkDuplicates Tracking 68458 as yet unmatched pairs. 68458 records in RAM. INFO 2016-05-17 17:45:42 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:8,183 INFO 2016-05-17 17:45:42 MarkDuplicates Tracking 28754 as yet unmatched pairs. 28754 records in RAM. INFO 2016-05-17 17:45:46 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:8,540 INFO 2016-05-17 17:45:46 MarkDuplicates Tracking 27466 as yet unmatched pairs. 27466 records in RAM. INFO 2016-05-17 17:45:54 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 8s. Last read position: mm9_chrM:8,852 INFO 2016-05-17 17:45:54 MarkDuplicates Tracking 62716 as yet unmatched pairs. 62716 records in RAM. INFO 2016-05-17 17:45:58 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:9,179 INFO 2016-05-17 17:45:58 MarkDuplicates Tracking 41572 as yet unmatched pairs. 41572 records in RAM. INFO 2016-05-17 17:46:12 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 14s. Last read position: mm9_chrM:9,635 INFO 2016-05-17 17:46:12 MarkDuplicates Tracking 57380 as yet unmatched pairs. 57380 records in RAM. INFO 2016-05-17 17:46:16 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:10,058 INFO 2016-05-17 17:46:16 MarkDuplicates Tracking 49524 as yet unmatched pairs. 49524 records in RAM. INFO 2016-05-17 17:46:20 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:10,419 INFO 2016-05-17 17:46:20 MarkDuplicates Tracking 63152 as yet unmatched pairs. 63152 records in RAM. INFO 2016-05-17 17:46:23 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:10,804 INFO 2016-05-17 17:46:23 MarkDuplicates Tracking 73698 as yet unmatched pairs. 73698 records in RAM. INFO 2016-05-17 17:46:27 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,055 INFO 2016-05-17 17:46:27 MarkDuplicates Tracking 109630 as yet unmatched pairs. 109630 records in RAM. INFO 2016-05-17 17:46:31 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,212 INFO 2016-05-17 17:46:31 MarkDuplicates Tracking 55282 as yet unmatched pairs. 55282 records in RAM. INFO 2016-05-17 17:46:35 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,415 INFO 2016-05-17 17:46:35 MarkDuplicates Tracking 55946 as yet unmatched pairs. 55946 records in RAM. INFO 2016-05-17 17:46:39 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,619 INFO 2016-05-17 17:46:39 MarkDuplicates Tracking 145248 as yet unmatched pairs. 145248 records in RAM. INFO 2016-05-17 17:46:43 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:11,841 INFO 2016-05-17 17:46:43 MarkDuplicates Tracking 81890 as yet unmatched pairs. 81890 records in RAM. INFO 2016-05-17 17:46:49 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 6s. Last read position: mm9_chrM:12,021 INFO 2016-05-17 17:46:49 MarkDuplicates Tracking 94472 as yet unmatched pairs. 94472 records in RAM. INFO 2016-05-17 17:46:53 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:12,216 INFO 2016-05-17 17:46:53 MarkDuplicates Tracking 60804 as yet unmatched pairs. 60804 records in RAM. INFO 2016-05-17 17:46:57 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:12,415 INFO 2016-05-17 17:46:57 MarkDuplicates Tracking 29662 as yet unmatched pairs. 29662 records in RAM. INFO 2016-05-17 17:47:01 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:12,611 INFO 2016-05-17 17:47:01 MarkDuplicates Tracking 102764 as yet unmatched pairs. 102764 records in RAM. INFO 2016-05-17 17:47:05 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:12,798 INFO 2016-05-17 17:47:05 MarkDuplicates Tracking 141230 as yet unmatched pairs. 141230 records in RAM. INFO 2016-05-17 17:47:09 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:12,991 INFO 2016-05-17 17:47:09 MarkDuplicates Tracking 71138 as yet unmatched pairs. 71138 records in RAM. INFO 2016-05-17 17:47:16 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 7s. Last read position: mm9_chrM:13,225 INFO 2016-05-17 17:47:16 MarkDuplicates Tracking 97042 as yet unmatched pairs. 97042 records in RAM. INFO 2016-05-17 17:47:20 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:13,437 INFO 2016-05-17 17:47:20 MarkDuplicates Tracking 107058 as yet unmatched pairs. 107058 records in RAM. INFO 2016-05-17 17:47:24 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:13,638 INFO 2016-05-17 17:47:24 MarkDuplicates Tracking 53864 as yet unmatched pairs. 53864 records in RAM. INFO 2016-05-17 17:47:28 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:13,851 INFO 2016-05-17 17:47:28 MarkDuplicates Tracking 72812 as yet unmatched pairs. 72812 records in RAM. INFO 2016-05-17 17:47:32 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 4s. Last read position: mm9_chrM:14,083 INFO 2016-05-17 17:47:32 MarkDuplicates Tracking 126988 as yet unmatched pairs. 126988 records in RAM. INFO 2016-05-17 17:47:36 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:14,263 INFO 2016-05-17 17:47:36 MarkDuplicates Tracking 78870 as yet unmatched pairs. 78870 records in RAM. INFO 2016-05-17 17:47:40 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:14,445 INFO 2016-05-17 17:47:40 MarkDuplicates Tracking 84480 as yet unmatched pairs. 84480 records in RAM. INFO 2016-05-17 17:47:44 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:14,608 INFO 2016-05-17 17:47:44 MarkDuplicates Tracking 75418 as yet unmatched pairs. 75418 records in RAM. INFO 2016-05-17 17:47:51 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 7s. Last read position: mm9_chrM:14,810 INFO 2016-05-17 17:47:51 MarkDuplicates Tracking 81190 as yet unmatched pairs. 81190 records in RAM. INFO 2016-05-17 17:47:55 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:15,005 INFO 2016-05-17 17:47:55 MarkDuplicates Tracking 61358 as yet unmatched pairs. 61358 records in RAM. INFO 2016-05-17 17:47:59 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:15,198 INFO 2016-05-17 17:47:59 MarkDuplicates Tracking 101292 as yet unmatched pairs. 101292 records in RAM. INFO 2016-05-17 17:48:03 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:15,378 INFO 2016-05-17 17:48:03 MarkDuplicates Tracking 69752 as yet unmatched pairs. 69752 records in RAM. INFO 2016-05-17 17:48:06 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:15,591 INFO 2016-05-17 17:48:06 MarkDuplicates Tracking 68804 as yet unmatched pairs. 68804 records in RAM. INFO 2016-05-17 17:48:10 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 3s. Last read position: mm9_chrM:16,231 INFO 2016-05-17 17:48:10 MarkDuplicates Tracking 14918 as yet unmatched pairs. 14918 records in RAM. INFO 2016-05-17 17:48:14 MarkDuplicates Read 175786350 records. 0 pairs never matched. INFO 2016-05-17 17:48:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 4066666440; totalMemory: 4094164992; maxMemory: 4094164992 INFO 2016-05-17 17:48:24 MarkDuplicates Will retain up to 127942656 duplicate indices before spilling to disk. INFO 2016-05-17 17:48:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-05-17 17:49:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-05-17 17:50:00 MarkDuplicates Sorting list of duplicate records. INFO 2016-05-17 17:50:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 3142732480; totalMemory: 4194304000; maxMemory: 4194304000 INFO 2016-05-17 17:50:08 MarkDuplicates Marking 124767702 records as duplicates. INFO 2016-05-17 17:50:08 MarkDuplicates Found 38524824 optical duplicate clusters. INFO 2016-05-17 17:51:55 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:44s. Time for last 10,000,000: 104s. Last read position: chr20:51,110,997 INFO 2016-05-17 17:53:50 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 114s. Last read position: chrM:1,336 INFO 2016-05-17 17:55:30 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 100s. Last read position: chrM:5,789 INFO 2016-05-17 17:57:10 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:06:59s. Time for last 10,000,000: 99s. Last read position: chrM:9,589 INFO 2016-05-17 17:58:48 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:08:37s. Time for last 10,000,000: 98s. Last read position: chrM:12,537 INFO 2016-05-17 18:00:24 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:10:13s. Time for last 10,000,000: 95s. Last read position: chrM:15,767 INFO 2016-05-17 18:02:15 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:12:04s. Time for last 10,000,000: 111s. Last read position: mm9_chr14:55,042,357 INFO 2016-05-17 18:04:05 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:13:54s. Time for last 10,000,000: 110s. Last read position: mm9_chr1:24,619,564 INFO 2016-05-17 18:05:48 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:15:37s. Time for last 10,000,000: 102s. Last read position: mm9_chr1:107,710,266 INFO 2016-05-17 18:07:49 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:17:38s. Time for last 10,000,000: 121s. Last read position: mm9_chr5:74,867,694 INFO 2016-05-17 18:09:53 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:19:42s. Time for last 10,000,000: 123s. Last read position: mm9_chrM:343 INFO 2016-05-17 18:11:42 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:21:30s. Time for last 10,000,000: 108s. Last read position: mm9_chrM:2,677 INFO 2016-05-17 18:13:27 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:23:16s. Time for last 10,000,000: 105s. Last read position: mm9_chrM:4,529 INFO 2016-05-17 18:15:16 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:25:05s. Time for last 10,000,000: 109s. Last read position: mm9_chrM:6,997 INFO 2016-05-17 18:17:04 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:26:53s. Time for last 10,000,000: 107s. Last read position: mm9_chrM:10,804 INFO 2016-05-17 18:18:53 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:28:42s. Time for last 10,000,000: 109s. Last read position: mm9_chrM:12,798 INFO 2016-05-17 18:20:43 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:30:32s. Time for last 10,000,000: 109s. Last read position: mm9_chrM:14,810 INFO 2016-05-17 18:21:48 MarkDuplicates Before output close freeMemory: 4213812720; totalMemory: 4244111360; maxMemory: 4244111360 INFO 2016-05-17 18:21:48 MarkDuplicates After output close freeMemory: 4213811664; totalMemory: 4244111360; maxMemory: 4244111360 [Tue May 17 18:21:48 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 48.30 minutes. Runtime.totalMemory()=4244111360 [bam_sort_core] merging from 72 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 323
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 325
samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 24 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 427
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 430
bedtools bamtobed -bedpe -mate1 -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 467
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 469
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz
# SYS command. line 472
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 250
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 253
nlines=$( zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | wc -l )
# SYS command. line 254
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 258
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.
# SYS command. line 261
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}' "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00" | \
gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.00
# SYS command. line 264
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}' "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01" | \
gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
# SYS command. line 266
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.01
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 91
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 167
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 171
Rscript $(which run_spp_nodups.R) -rf \
-c=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc -speak=0
# SYS command. line 174
sed -r 's/,[^\t]+//g' /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp
# SYS command. line 175
mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf
result filename: /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
opened /tmp/Rtmpo7id9T/3hr_rep2_merged_R1.trim.PE2SE.nodup.25.tagAlign9e967bf41d5d
done. read 25000000 fragments
ChIP data read length 75
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.140628
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.225250363400632
Top 3 estimates for fragment length 0
Window half size 430
Phantom peak location 80
Phantom peak Correlation 0.2449688
Normalized Strand cross-correlation coefficient (NSC) 1.601747
Relative Strand Cross correlation Coefficient (RSC) 0.811019
Phantom Peak Quality Tag 0
null device
1
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Loading required package: caTools
| ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH INFO @ Tue, 17 May 2016 12:53:50: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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 @ Tue, 17 May 2016 12:53:50: #1 read tag files... INFO @ Tue, 17 May 2016 12:53:50: #1 read treatment tags... INFO @ Tue, 17 May 2016 12:53:52: 1000000 INFO @ Tue, 17 May 2016 12:53:54: 2000000 INFO @ Tue, 17 May 2016 12:53:56: 3000000 INFO @ Tue, 17 May 2016 12:53:59: 4000000 INFO @ Tue, 17 May 2016 12:54:01: 5000000 INFO @ Tue, 17 May 2016 12:54:03: 6000000 INFO @ Tue, 17 May 2016 12:54:05: 7000000 INFO @ Tue, 17 May 2016 12:54:07: 8000000 INFO @ Tue, 17 May 2016 12:54:09: 9000000 INFO @ Tue, 17 May 2016 12:54:11: 10000000 INFO @ Tue, 17 May 2016 12:54:14: 11000000 INFO @ Tue, 17 May 2016 12:54:16: 12000000 INFO @ Tue, 17 May 2016 12:54:18: 13000000 INFO @ Tue, 17 May 2016 12:54:20: 14000000 INFO @ Tue, 17 May 2016 12:54:22: 15000000 INFO @ Tue, 17 May 2016 12:54:24: 16000000 INFO @ Tue, 17 May 2016 12:54:26: 17000000 INFO @ Tue, 17 May 2016 12:54:28: 18000000 INFO @ Tue, 17 May 2016 12:54:30: 19000000 INFO @ Tue, 17 May 2016 12:54:33: 20000000 INFO @ Tue, 17 May 2016 12:54:35: 21000000 INFO @ Tue, 17 May 2016 12:54:37: 22000000 INFO @ Tue, 17 May 2016 12:54:39: 23000000 INFO @ Tue, 17 May 2016 12:54:41: 24000000 INFO @ Tue, 17 May 2016 12:54:43: 25000000 INFO @ Tue, 17 May 2016 12:54:45: 26000000 INFO @ Tue, 17 May 2016 12:54:47: 27000000 INFO @ Tue, 17 May 2016 12:54:49: 28000000 INFO @ Tue, 17 May 2016 12:54:52: 29000000 INFO @ Tue, 17 May 2016 12:54:54: #1 tag size is determined as 51 bps INFO @ Tue, 17 May 2016 12:54:54: #1 tag size = 51 INFO @ Tue, 17 May 2016 12:54:54: #1 total tags in treatment: 29044736 INFO @ Tue, 17 May 2016 12:54:54: #1 finished! INFO @ Tue, 17 May 2016 12:54:54: #2 Build Peak Model... INFO @ Tue, 17 May 2016 12:54:54: #2 Skipped... INFO @ Tue, 17 May 2016 12:54:54: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 12:54:54: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 12:54:54: #3 Call peaks... INFO @ Tue, 17 May 2016 12:54:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... INFO @ Tue, 17 May 2016 12:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 12:56:21: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 12:58:21: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 12:58:25: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak INFO @ Tue, 17 May 2016 12:58:28: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak INFO @ Tue, 17 May 2016 12:58:31: Done! INFO @ Tue, 17 May 2016 12:58:42: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.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 @ Tue, 17 May 2016 12:58:42: #1 read tag files... INFO @ Tue, 17 May 2016 12:58:42: #1 read treatment tags... INFO @ Tue, 17 May 2016 12:58:44: 1000000 INFO @ Tue, 17 May 2016 12:58:46: 2000000 INFO @ Tue, 17 May 2016 12:58:48: 3000000 INFO @ Tue, 17 May 2016 12:58:50: 4000000 INFO @ Tue, 17 May 2016 12:58:52: 5000000 INFO @ Tue, 17 May 2016 12:58:54: 6000000 INFO @ Tue, 17 May 2016 12:58:56: 7000000 INFO @ Tue, 17 May 2016 12:58:58: 8000000 INFO @ Tue, 17 May 2016 12:59:00: 9000000 INFO @ Tue, 17 May 2016 12:59:02: 10000000 INFO @ Tue, 17 May 2016 12:59:04: 11000000 INFO @ Tue, 17 May 2016 12:59:06: 12000000 INFO @ Tue, 17 May 2016 12:59:08: 13000000 INFO @ Tue, 17 May 2016 12:59:10: 14000000 INFO @ Tue, 17 May 2016 12:59:12: 15000000 INFO @ Tue, 17 May 2016 12:59:14: 16000000 INFO @ Tue, 17 May 2016 12:59:16: 17000000 INFO @ Tue, 17 May 2016 12:59:18: 18000000 INFO @ Tue, 17 May 2016 12:59:20: 19000000 INFO @ Tue, 17 May 2016 12:59:22: 20000000 INFO @ Tue, 17 May 2016 12:59:24: 21000000 INFO @ Tue, 17 May 2016 12:59:26: 22000000 INFO @ Tue, 17 May 2016 12:59:28: 23000000 INFO @ Tue, 17 May 2016 12:59:30: 24000000 INFO @ Tue, 17 May 2016 12:59:32: 25000000 INFO @ Tue, 17 May 2016 12:59:34: 26000000 INFO @ Tue, 17 May 2016 12:59:36: 27000000 INFO @ Tue, 17 May 2016 12:59:38: 28000000 INFO @ Tue, 17 May 2016 12:59:40: 29000000 INFO @ Tue, 17 May 2016 12:59:43: #1 tag size is determined as 51 bps INFO @ Tue, 17 May 2016 12:59:43: #1 tag size = 51 INFO @ Tue, 17 May 2016 12:59:43: #1 total tags in treatment: 29044736 INFO @ Tue, 17 May 2016 12:59:43: #1 finished! INFO @ Tue, 17 May 2016 12:59:43: #2 Build Peak Model... INFO @ Tue, 17 May 2016 12:59:43: #2 Skipped... INFO @ Tue, 17 May 2016 12:59:43: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 12:59:43: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 12:59:43: #3 Call peaks... INFO @ Tue, 17 May 2016 12:59:43: #3 Going to call summits inside each peak ... INFO @ Tue, 17 May 2016 12:59:43: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... INFO @ Tue, 17 May 2016 12:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:01:10: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Tue, 17 May 2016 13:01:10: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg INFO @ Tue, 17 May 2016 13:01:10: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg INFO @ Tue, 17 May 2016 13:01:10: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Tue, 17 May 2016 13:01:10: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:08:27: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 13:08:33: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak INFO @ Tue, 17 May 2016 13:08:38: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed INFO @ Tue, 17 May 2016 13:08:40: Done! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH INFO @ Tue, 17 May 2016 12:53:50: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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 @ Tue, 17 May 2016 12:53:50: #1 read tag files... INFO @ Tue, 17 May 2016 12:53:50: #1 read treatment tags... INFO @ Tue, 17 May 2016 12:53:52: 1000000 INFO @ Tue, 17 May 2016 12:53:54: 2000000 INFO @ Tue, 17 May 2016 12:53:56: 3000000 INFO @ Tue, 17 May 2016 12:53:58: 4000000 INFO @ Tue, 17 May 2016 12:54:00: 5000000 INFO @ Tue, 17 May 2016 12:54:02: 6000000 INFO @ Tue, 17 May 2016 12:54:04: 7000000 INFO @ Tue, 17 May 2016 12:54:06: 8000000 INFO @ Tue, 17 May 2016 12:54:08: 9000000 INFO @ Tue, 17 May 2016 12:54:10: 10000000 INFO @ Tue, 17 May 2016 12:54:12: 11000000 INFO @ Tue, 17 May 2016 12:54:14: 12000000 INFO @ Tue, 17 May 2016 12:54:16: 13000000 INFO @ Tue, 17 May 2016 12:54:18: 14000000 INFO @ Tue, 17 May 2016 12:54:20: 15000000 INFO @ Tue, 17 May 2016 12:54:22: 16000000 INFO @ Tue, 17 May 2016 12:54:24: 17000000 INFO @ Tue, 17 May 2016 12:54:26: 18000000 INFO @ Tue, 17 May 2016 12:54:28: 19000000 INFO @ Tue, 17 May 2016 12:54:30: 20000000 INFO @ Tue, 17 May 2016 12:54:32: 21000000 INFO @ Tue, 17 May 2016 12:54:34: 22000000 INFO @ Tue, 17 May 2016 12:54:36: 23000000 INFO @ Tue, 17 May 2016 12:54:38: 24000000 INFO @ Tue, 17 May 2016 12:54:40: 25000000 INFO @ Tue, 17 May 2016 12:54:42: 26000000 INFO @ Tue, 17 May 2016 12:54:44: 27000000 INFO @ Tue, 17 May 2016 12:54:46: 28000000 INFO @ Tue, 17 May 2016 12:54:48: 29000000 INFO @ Tue, 17 May 2016 12:54:50: #1 tag size is determined as 68 bps INFO @ Tue, 17 May 2016 12:54:50: #1 tag size = 68 INFO @ Tue, 17 May 2016 12:54:50: #1 total tags in treatment: 29044734 INFO @ Tue, 17 May 2016 12:54:50: #1 finished! INFO @ Tue, 17 May 2016 12:54:50: #2 Build Peak Model... INFO @ Tue, 17 May 2016 12:54:50: #2 Skipped... INFO @ Tue, 17 May 2016 12:54:50: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 12:54:50: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 12:54:50: #3 Call peaks... INFO @ Tue, 17 May 2016 12:54:50: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... INFO @ Tue, 17 May 2016 12:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 12:56:17: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 12:58:25: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 12:58:29: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak INFO @ Tue, 17 May 2016 12:58:32: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak INFO @ Tue, 17 May 2016 12:58:35: Done! INFO @ Tue, 17 May 2016 12:58:46: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.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 @ Tue, 17 May 2016 12:58:46: #1 read tag files... INFO @ Tue, 17 May 2016 12:58:46: #1 read treatment tags... INFO @ Tue, 17 May 2016 12:58:48: 1000000 INFO @ Tue, 17 May 2016 12:58:50: 2000000 INFO @ Tue, 17 May 2016 12:58:52: 3000000 INFO @ Tue, 17 May 2016 12:58:54: 4000000 INFO @ Tue, 17 May 2016 12:58:56: 5000000 INFO @ Tue, 17 May 2016 12:58:58: 6000000 INFO @ Tue, 17 May 2016 12:59:00: 7000000 INFO @ Tue, 17 May 2016 12:59:02: 8000000 INFO @ Tue, 17 May 2016 12:59:04: 9000000 INFO @ Tue, 17 May 2016 12:59:06: 10000000 INFO @ Tue, 17 May 2016 12:59:08: 11000000 INFO @ Tue, 17 May 2016 12:59:10: 12000000 INFO @ Tue, 17 May 2016 12:59:12: 13000000 INFO @ Tue, 17 May 2016 12:59:14: 14000000 INFO @ Tue, 17 May 2016 12:59:16: 15000000 INFO @ Tue, 17 May 2016 12:59:18: 16000000 INFO @ Tue, 17 May 2016 12:59:20: 17000000 INFO @ Tue, 17 May 2016 12:59:22: 18000000 INFO @ Tue, 17 May 2016 12:59:24: 19000000 INFO @ Tue, 17 May 2016 12:59:26: 20000000 INFO @ Tue, 17 May 2016 12:59:28: 21000000 INFO @ Tue, 17 May 2016 12:59:30: 22000000 INFO @ Tue, 17 May 2016 12:59:32: 23000000 INFO @ Tue, 17 May 2016 12:59:34: 24000000 INFO @ Tue, 17 May 2016 12:59:36: 25000000 INFO @ Tue, 17 May 2016 12:59:38: 26000000 INFO @ Tue, 17 May 2016 12:59:40: 27000000 INFO @ Tue, 17 May 2016 12:59:42: 28000000 INFO @ Tue, 17 May 2016 12:59:44: 29000000 INFO @ Tue, 17 May 2016 12:59:47: #1 tag size is determined as 68 bps INFO @ Tue, 17 May 2016 12:59:47: #1 tag size = 68 INFO @ Tue, 17 May 2016 12:59:47: #1 total tags in treatment: 29044734 INFO @ Tue, 17 May 2016 12:59:47: #1 finished! INFO @ Tue, 17 May 2016 12:59:47: #2 Build Peak Model... INFO @ Tue, 17 May 2016 12:59:47: #2 Skipped... INFO @ Tue, 17 May 2016 12:59:47: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 12:59:47: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 12:59:47: #3 Call peaks... INFO @ Tue, 17 May 2016 12:59:47: #3 Going to call summits inside each peak ... INFO @ Tue, 17 May 2016 12:59:47: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... INFO @ Tue, 17 May 2016 12:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:01:14: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Tue, 17 May 2016 13:01:14: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg INFO @ Tue, 17 May 2016 13:01:14: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg INFO @ Tue, 17 May 2016 13:01:14: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Tue, 17 May 2016 13:01:14: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:08:40: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 13:08:47: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak INFO @ Tue, 17 May 2016 13:08:51: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/pseudo_reps/rep1/pr2/3hr_rep2_merged_R1.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed INFO @ Tue, 17 May 2016 13:08:53: Done! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH INFO @ Tue, 17 May 2016 13:09:02: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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 @ Tue, 17 May 2016 13:09:02: #1 read tag files... INFO @ Tue, 17 May 2016 13:09:02: #1 read treatment tags... INFO @ Tue, 17 May 2016 13:09:04: 1000000 INFO @ Tue, 17 May 2016 13:09:06: 2000000 INFO @ Tue, 17 May 2016 13:09:08: 3000000 INFO @ Tue, 17 May 2016 13:09:10: 4000000 INFO @ Tue, 17 May 2016 13:09:12: 5000000 INFO @ Tue, 17 May 2016 13:09:14: 6000000 INFO @ Tue, 17 May 2016 13:09:16: 7000000 INFO @ Tue, 17 May 2016 13:09:18: 8000000 INFO @ Tue, 17 May 2016 13:09:20: 9000000 INFO @ Tue, 17 May 2016 13:09:22: 10000000 INFO @ Tue, 17 May 2016 13:09:24: 11000000 INFO @ Tue, 17 May 2016 13:09:25: 12000000 INFO @ Tue, 17 May 2016 13:09:27: 13000000 INFO @ Tue, 17 May 2016 13:09:29: 14000000 INFO @ Tue, 17 May 2016 13:09:31: 15000000 INFO @ Tue, 17 May 2016 13:09:33: 16000000 INFO @ Tue, 17 May 2016 13:09:35: 17000000 INFO @ Tue, 17 May 2016 13:09:37: 18000000 INFO @ Tue, 17 May 2016 13:09:39: 19000000 INFO @ Tue, 17 May 2016 13:09:41: 20000000 INFO @ Tue, 17 May 2016 13:09:43: 21000000 INFO @ Tue, 17 May 2016 13:09:45: 22000000 INFO @ Tue, 17 May 2016 13:09:47: 23000000 INFO @ Tue, 17 May 2016 13:09:48: 24000000 INFO @ Tue, 17 May 2016 13:09:50: 25000000 INFO @ Tue, 17 May 2016 13:09:52: 26000000 INFO @ Tue, 17 May 2016 13:09:54: 27000000 INFO @ Tue, 17 May 2016 13:09:56: 28000000 INFO @ Tue, 17 May 2016 13:09:58: 29000000 INFO @ Tue, 17 May 2016 13:10:00: 30000000 INFO @ Tue, 17 May 2016 13:10:02: 31000000 INFO @ Tue, 17 May 2016 13:10:04: 32000000 INFO @ Tue, 17 May 2016 13:10:06: 33000000 INFO @ Tue, 17 May 2016 13:10:08: 34000000 INFO @ Tue, 17 May 2016 13:10:09: 35000000 INFO @ Tue, 17 May 2016 13:10:11: 36000000 INFO @ Tue, 17 May 2016 13:10:13: 37000000 INFO @ Tue, 17 May 2016 13:10:15: 38000000 INFO @ Tue, 17 May 2016 13:10:17: 39000000 INFO @ Tue, 17 May 2016 13:10:19: 40000000 INFO @ Tue, 17 May 2016 13:10:21: 41000000 INFO @ Tue, 17 May 2016 13:10:23: 42000000 INFO @ Tue, 17 May 2016 13:10:25: 43000000 INFO @ Tue, 17 May 2016 13:10:27: 44000000 INFO @ Tue, 17 May 2016 13:10:28: 45000000 INFO @ Tue, 17 May 2016 13:10:30: 46000000 INFO @ Tue, 17 May 2016 13:10:32: 47000000 INFO @ Tue, 17 May 2016 13:10:34: 48000000 INFO @ Tue, 17 May 2016 13:10:36: 49000000 INFO @ Tue, 17 May 2016 13:10:38: 50000000 INFO @ Tue, 17 May 2016 13:10:40: 51000000 INFO @ Tue, 17 May 2016 13:10:42: 52000000 INFO @ Tue, 17 May 2016 13:10:48: #1 tag size is determined as 67 bps INFO @ Tue, 17 May 2016 13:10:48: #1 tag size = 67 INFO @ Tue, 17 May 2016 13:10:48: #1 total tags in treatment: 52989484 INFO @ Tue, 17 May 2016 13:10:48: #1 finished! INFO @ Tue, 17 May 2016 13:10:48: #2 Build Peak Model... INFO @ Tue, 17 May 2016 13:10:48: #2 Skipped... INFO @ Tue, 17 May 2016 13:10:48: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 13:10:48: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 13:10:48: #3 Call peaks... INFO @ Tue, 17 May 2016 13:10:48: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... INFO @ Tue, 17 May 2016 13:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:12:58: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:16:02: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 13:16:05: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak INFO @ Tue, 17 May 2016 13:16:08: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak INFO @ Tue, 17 May 2016 13:16:10: Done! INFO @ Tue, 17 May 2016 13:16:24: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1 # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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 @ Tue, 17 May 2016 13:16:24: #1 read tag files... INFO @ Tue, 17 May 2016 13:16:24: #1 read treatment tags... INFO @ Tue, 17 May 2016 13:16:26: 1000000 INFO @ Tue, 17 May 2016 13:16:28: 2000000 INFO @ Tue, 17 May 2016 13:16:30: 3000000 INFO @ Tue, 17 May 2016 13:16:32: 4000000 INFO @ Tue, 17 May 2016 13:16:34: 5000000 INFO @ Tue, 17 May 2016 13:16:36: 6000000 INFO @ Tue, 17 May 2016 13:16:38: 7000000 INFO @ Tue, 17 May 2016 13:16:40: 8000000 INFO @ Tue, 17 May 2016 13:16:42: 9000000 INFO @ Tue, 17 May 2016 13:16:44: 10000000 INFO @ Tue, 17 May 2016 13:16:46: 11000000 INFO @ Tue, 17 May 2016 13:16:48: 12000000 INFO @ Tue, 17 May 2016 13:16:50: 13000000 INFO @ Tue, 17 May 2016 13:16:51: 14000000 INFO @ Tue, 17 May 2016 13:16:53: 15000000 INFO @ Tue, 17 May 2016 13:16:55: 16000000 INFO @ Tue, 17 May 2016 13:16:57: 17000000 INFO @ Tue, 17 May 2016 13:16:59: 18000000 INFO @ Tue, 17 May 2016 13:17:01: 19000000 INFO @ Tue, 17 May 2016 13:17:04: 20000000 INFO @ Tue, 17 May 2016 13:17:06: 21000000 INFO @ Tue, 17 May 2016 13:17:08: 22000000 INFO @ Tue, 17 May 2016 13:17:10: 23000000 INFO @ Tue, 17 May 2016 13:17:12: 24000000 INFO @ Tue, 17 May 2016 13:17:14: 25000000 INFO @ Tue, 17 May 2016 13:17:16: 26000000 INFO @ Tue, 17 May 2016 13:17:18: 27000000 INFO @ Tue, 17 May 2016 13:17:20: 28000000 INFO @ Tue, 17 May 2016 13:17:22: 29000000 INFO @ Tue, 17 May 2016 13:17:24: 30000000 INFO @ Tue, 17 May 2016 13:17:26: 31000000 INFO @ Tue, 17 May 2016 13:17:28: 32000000 INFO @ Tue, 17 May 2016 13:17:30: 33000000 INFO @ Tue, 17 May 2016 13:17:32: 34000000 INFO @ Tue, 17 May 2016 13:17:34: 35000000 INFO @ Tue, 17 May 2016 13:17:36: 36000000 INFO @ Tue, 17 May 2016 13:17:38: 37000000 INFO @ Tue, 17 May 2016 13:17:40: 38000000 INFO @ Tue, 17 May 2016 13:17:42: 39000000 INFO @ Tue, 17 May 2016 13:17:44: 40000000 INFO @ Tue, 17 May 2016 13:17:46: 41000000 INFO @ Tue, 17 May 2016 13:17:48: 42000000 INFO @ Tue, 17 May 2016 13:17:50: 43000000 INFO @ Tue, 17 May 2016 13:17:52: 44000000 INFO @ Tue, 17 May 2016 13:17:54: 45000000 INFO @ Tue, 17 May 2016 13:17:56: 46000000 INFO @ Tue, 17 May 2016 13:17:58: 47000000 INFO @ Tue, 17 May 2016 13:18:00: 48000000 INFO @ Tue, 17 May 2016 13:18:02: 49000000 INFO @ Tue, 17 May 2016 13:18:04: 50000000 INFO @ Tue, 17 May 2016 13:18:06: 51000000 INFO @ Tue, 17 May 2016 13:18:08: 52000000 INFO @ Tue, 17 May 2016 13:18:15: #1 tag size is determined as 67 bps INFO @ Tue, 17 May 2016 13:18:15: #1 tag size = 67 INFO @ Tue, 17 May 2016 13:18:15: #1 total tags in treatment: 52989484 INFO @ Tue, 17 May 2016 13:18:15: #1 finished! INFO @ Tue, 17 May 2016 13:18:15: #2 Build Peak Model... INFO @ Tue, 17 May 2016 13:18:15: #2 Skipped... INFO @ Tue, 17 May 2016 13:18:15: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 13:18:15: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 13:18:15: #3 Call peaks... INFO @ Tue, 17 May 2016 13:18:15: #3 Going to call summits inside each peak ... INFO @ Tue, 17 May 2016 13:18:15: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... INFO @ Tue, 17 May 2016 13:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:20:39: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Tue, 17 May 2016 13:20:39: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg INFO @ Tue, 17 May 2016 13:20:39: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg INFO @ Tue, 17 May 2016 13:20:39: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Tue, 17 May 2016 13:20:39: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:30:01: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls INFO @ Tue, 17 May 2016 13:30:06: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak INFO @ Tue, 17 May 2016 13:30:11: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed INFO @ Tue, 17 May 2016 13:30:13: Done! | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m FE;\
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" -b 0 | bedClip stdin "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph "/srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes" "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH INFO @ Tue, 17 May 2016 13:09:02: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all # ARGUMENTS LIST: # name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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 @ Tue, 17 May 2016 13:09:02: #1 read tag files... INFO @ Tue, 17 May 2016 13:09:02: #1 read treatment tags... INFO @ Tue, 17 May 2016 13:09:04: 1000000 INFO @ Tue, 17 May 2016 13:09:06: 2000000 INFO @ Tue, 17 May 2016 13:09:08: 3000000 INFO @ Tue, 17 May 2016 13:09:10: 4000000 INFO @ Tue, 17 May 2016 13:09:12: 5000000 INFO @ Tue, 17 May 2016 13:09:14: 6000000 INFO @ Tue, 17 May 2016 13:09:16: 7000000 INFO @ Tue, 17 May 2016 13:09:18: 8000000 INFO @ Tue, 17 May 2016 13:09:20: 9000000 INFO @ Tue, 17 May 2016 13:09:22: 10000000 INFO @ Tue, 17 May 2016 13:09:24: 11000000 INFO @ Tue, 17 May 2016 13:09:26: 12000000 INFO @ Tue, 17 May 2016 13:09:28: 13000000 INFO @ Tue, 17 May 2016 13:09:30: 14000000 INFO @ Tue, 17 May 2016 13:09:32: 15000000 INFO @ Tue, 17 May 2016 13:09:33: 16000000 INFO @ Tue, 17 May 2016 13:09:35: 17000000 INFO @ Tue, 17 May 2016 13:09:37: 18000000 INFO @ Tue, 17 May 2016 13:09:39: 19000000 INFO @ Tue, 17 May 2016 13:09:41: 20000000 INFO @ Tue, 17 May 2016 13:09:43: 21000000 INFO @ Tue, 17 May 2016 13:09:45: 22000000 INFO @ Tue, 17 May 2016 13:09:47: 23000000 INFO @ Tue, 17 May 2016 13:09:49: 24000000 INFO @ Tue, 17 May 2016 13:09:51: 25000000 INFO @ Tue, 17 May 2016 13:09:53: 26000000 INFO @ Tue, 17 May 2016 13:09:55: 27000000 INFO @ Tue, 17 May 2016 13:09:57: 28000000 INFO @ Tue, 17 May 2016 13:09:59: 29000000 INFO @ Tue, 17 May 2016 13:10:01: 30000000 INFO @ Tue, 17 May 2016 13:10:02: 31000000 INFO @ Tue, 17 May 2016 13:10:04: 32000000 INFO @ Tue, 17 May 2016 13:10:06: 33000000 INFO @ Tue, 17 May 2016 13:10:08: 34000000 INFO @ Tue, 17 May 2016 13:10:10: 35000000 INFO @ Tue, 17 May 2016 13:10:12: 36000000 INFO @ Tue, 17 May 2016 13:10:14: 37000000 INFO @ Tue, 17 May 2016 13:10:16: 38000000 INFO @ Tue, 17 May 2016 13:10:18: 39000000 INFO @ Tue, 17 May 2016 13:10:20: 40000000 INFO @ Tue, 17 May 2016 13:10:22: 41000000 INFO @ Tue, 17 May 2016 13:10:24: 42000000 INFO @ Tue, 17 May 2016 13:10:25: 43000000 INFO @ Tue, 17 May 2016 13:10:27: 44000000 INFO @ Tue, 17 May 2016 13:10:29: 45000000 INFO @ Tue, 17 May 2016 13:10:31: 46000000 INFO @ Tue, 17 May 2016 13:10:33: 47000000 INFO @ Tue, 17 May 2016 13:10:35: 48000000 INFO @ Tue, 17 May 2016 13:10:37: 49000000 INFO @ Tue, 17 May 2016 13:10:39: 50000000 INFO @ Tue, 17 May 2016 13:10:41: 51000000 INFO @ Tue, 17 May 2016 13:10:43: 52000000 INFO @ Tue, 17 May 2016 13:10:49: #1 tag size is determined as 67 bps INFO @ Tue, 17 May 2016 13:10:49: #1 tag size = 67 INFO @ Tue, 17 May 2016 13:10:49: #1 total tags in treatment: 52989484 INFO @ Tue, 17 May 2016 13:10:49: #1 finished! INFO @ Tue, 17 May 2016 13:10:49: #2 Build Peak Model... INFO @ Tue, 17 May 2016 13:10:49: #2 Skipped... INFO @ Tue, 17 May 2016 13:10:49: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 13:10:49: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 13:10:49: #3 Call peaks... INFO @ Tue, 17 May 2016 13:10:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... INFO @ Tue, 17 May 2016 13:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:13:02: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:15:44: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls INFO @ Tue, 17 May 2016 13:15:47: #4 Write broad peak in broadPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak INFO @ Tue, 17 May 2016 13:15:50: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak INFO @ Tue, 17 May 2016 13:15:52: Done! INFO @ Tue, 17 May 2016 13:16:07: # Command line: callpeak -t /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits # ARGUMENTS LIST: # name = /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf # format = BED # ChIP-seq file = ['/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.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 @ Tue, 17 May 2016 13:16:07: #1 read tag files... INFO @ Tue, 17 May 2016 13:16:07: #1 read treatment tags... INFO @ Tue, 17 May 2016 13:16:08: 1000000 INFO @ Tue, 17 May 2016 13:16:10: 2000000 INFO @ Tue, 17 May 2016 13:16:12: 3000000 INFO @ Tue, 17 May 2016 13:16:14: 4000000 INFO @ Tue, 17 May 2016 13:16:16: 5000000 INFO @ Tue, 17 May 2016 13:16:18: 6000000 INFO @ Tue, 17 May 2016 13:16:20: 7000000 INFO @ Tue, 17 May 2016 13:16:22: 8000000 INFO @ Tue, 17 May 2016 13:16:24: 9000000 INFO @ Tue, 17 May 2016 13:16:26: 10000000 INFO @ Tue, 17 May 2016 13:16:28: 11000000 INFO @ Tue, 17 May 2016 13:16:30: 12000000 INFO @ Tue, 17 May 2016 13:16:32: 13000000 INFO @ Tue, 17 May 2016 13:16:34: 14000000 INFO @ Tue, 17 May 2016 13:16:36: 15000000 INFO @ Tue, 17 May 2016 13:16:38: 16000000 INFO @ Tue, 17 May 2016 13:16:40: 17000000 INFO @ Tue, 17 May 2016 13:16:42: 18000000 INFO @ Tue, 17 May 2016 13:16:43: 19000000 INFO @ Tue, 17 May 2016 13:16:45: 20000000 INFO @ Tue, 17 May 2016 13:16:47: 21000000 INFO @ Tue, 17 May 2016 13:16:49: 22000000 INFO @ Tue, 17 May 2016 13:16:51: 23000000 INFO @ Tue, 17 May 2016 13:16:53: 24000000 INFO @ Tue, 17 May 2016 13:16:55: 25000000 INFO @ Tue, 17 May 2016 13:16:57: 26000000 INFO @ Tue, 17 May 2016 13:16:59: 27000000 INFO @ Tue, 17 May 2016 13:17:01: 28000000 INFO @ Tue, 17 May 2016 13:17:03: 29000000 INFO @ Tue, 17 May 2016 13:17:05: 30000000 INFO @ Tue, 17 May 2016 13:17:07: 31000000 INFO @ Tue, 17 May 2016 13:17:09: 32000000 INFO @ Tue, 17 May 2016 13:17:11: 33000000 INFO @ Tue, 17 May 2016 13:17:13: 34000000 INFO @ Tue, 17 May 2016 13:17:15: 35000000 INFO @ Tue, 17 May 2016 13:17:17: 36000000 INFO @ Tue, 17 May 2016 13:17:19: 37000000 INFO @ Tue, 17 May 2016 13:17:21: 38000000 INFO @ Tue, 17 May 2016 13:17:23: 39000000 INFO @ Tue, 17 May 2016 13:17:25: 40000000 INFO @ Tue, 17 May 2016 13:17:27: 41000000 INFO @ Tue, 17 May 2016 13:17:29: 42000000 INFO @ Tue, 17 May 2016 13:17:31: 43000000 INFO @ Tue, 17 May 2016 13:17:33: 44000000 INFO @ Tue, 17 May 2016 13:17:35: 45000000 INFO @ Tue, 17 May 2016 13:17:37: 46000000 INFO @ Tue, 17 May 2016 13:17:39: 47000000 INFO @ Tue, 17 May 2016 13:17:41: 48000000 INFO @ Tue, 17 May 2016 13:17:43: 49000000 INFO @ Tue, 17 May 2016 13:17:45: 50000000 INFO @ Tue, 17 May 2016 13:17:47: 51000000 INFO @ Tue, 17 May 2016 13:17:49: 52000000 INFO @ Tue, 17 May 2016 13:17:55: #1 tag size is determined as 67 bps INFO @ Tue, 17 May 2016 13:17:55: #1 tag size = 67 INFO @ Tue, 17 May 2016 13:17:55: #1 total tags in treatment: 52989484 INFO @ Tue, 17 May 2016 13:17:55: #1 finished! INFO @ Tue, 17 May 2016 13:17:55: #2 Build Peak Model... INFO @ Tue, 17 May 2016 13:17:55: #2 Skipped... INFO @ Tue, 17 May 2016 13:17:55: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Tue, 17 May 2016 13:17:55: #2 Use 150 as fragment length INFO @ Tue, 17 May 2016 13:17:55: #3 Call peaks... INFO @ Tue, 17 May 2016 13:17:55: #3 Going to call summits inside each peak ... INFO @ Tue, 17 May 2016 13:17:55: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ Tue, 17 May 2016 13:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 17 May 2016 13:20:25: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Tue, 17 May 2016 13:20:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg INFO @ Tue, 17 May 2016 13:20:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg INFO @ Tue, 17 May 2016 13:20:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. INFO @ Tue, 17 May 2016 13:20:25: #3 Call peaks for each chromosome... INFO @ Tue, 17 May 2016 13:27:35: #4 Write output xls file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.xls INFO @ Tue, 17 May 2016 13:27:38: #4 Write peak in narrowPeak format file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak INFO @ Tue, 17 May 2016 13:27:40: #4 Write summits bed file... /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_summits.bed INFO @ Tue, 17 May 2016 13:27:42: Done! INFO @ Tue, 17 May 2016 13:27:46: Read and build treatment bedGraph... INFO @ Tue, 17 May 2016 13:29:34: Read and build control bedGraph... INFO @ Tue, 17 May 2016 13:30:10: Build scoreTrackII... INFO @ Tue, 17 May 2016 13:30:49: Calculate scores comparing treatment and control by 'FE'... INFO @ Tue, 17 May 2016 13:36:27: Write bedGraph of scores... INFO @ Tue, 17 May 2016 13:39:39: Finished 'FE'! Please check '/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! Chromosome phiX174 isn't in /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes line 52217537 of stdin | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 323
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 325
samtools sort -n /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH [bam_sort_core] merging from 21 files... | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 427
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 430
bedtools bamtobed -bedpe -mate1 -i /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 467
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 469
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz
# SYS command. line 472
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 250
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 253
nlines=$( zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | wc -l )
# SYS command. line 254
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 258
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.
# SYS command. line 261
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}' "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00" | \
gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.00
# SYS command. line 264
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}' "/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01" | \
gzip -c > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tagAlign.gz
# SYS command. line 266
rm -f /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.01
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr1/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/pseudo_reps/rep2/pr2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 91
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
zcat /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.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/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 167
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 171
Rscript $(which run_spp_nodups.R) -rf \
-c=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc -speak=0
# SYS command. line 174
sed -r 's/,[^\t]+//g' /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp
# SYS command. line 175
mv /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.25.cc.qc
|
| Type | Name | Value |
|---|---|---|
| string | _ | /bin/sh |
| string | _JAVA_OPTIONS | -Xms256M -Xmx512M -XX:ParallelGCThreads=1 |
| bool | allowEmpty | false |
| string[] | args | [-multimapping, 4, -out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq] |
| string | BASSETDIR | /srv/scratch/annashch/Basset |
| bool | canFail | false |
| int | cpus | 1 |
| int | cpusLocal | 48 |
| string | CRC | /srv/scratch/annashch/crc |
| int | day | 86400 |
| string | DEEPLEARN_SCRIPTS_DIR | /srv/scratch/annashch/deeplearning_avanti |
| string | DEEPLIFT_DIR | /srv/scratch/annashch/deeplift/deeplift |
| real | E | 2.718281828459045 |
| string | EIGEN | /mnt/lab_data/montgomery/shared/Eigen |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/annashch/enhancer_prediction_code |
| int | G | 1073741824 |
| string | HOME | /users/annashch/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /users/annashch/keras |
| string | LANG | en_US.UTF-8 |
| string | LD_LIBRARY_PATH | /lib/x86_64-linux-gnu:/usr/local/cudnn/lib64: |
| string | LOADEDMODULES | |
| string | LOGNAME | annashch |
| string | LUACPATH | /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src: |
| string | LUAPATH | /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src: |
| int | M | 1048576 |
| string | /var/mail/annashch | |
| string | MALLOC_ARENA_MAX | 4 |
| string | MAX_JAVA_MEM | 20G |
| 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 | MODULESHOME | /software/env_module/3.2.10 |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/annashch/output |
| string | programName | atac.bds |
| string | programPath | /srv/scratch/annashch/bds_atac/atac.bds |
| string | PWD | /srv/scratch/annashch/output |
| string | PYTHONPATH | /users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/keras:/srv/scratch/annashch/Basset/src: |
| string | QT_QPA_PLATFORMTHEME | appmenu-qt5 |
| string | queue | |
| int | retry | 0 |
| string | SHELL | /bin/bash |
| string | SHLVL | 2 |
| string | SSH_CLIENT | 10.0.2.3 44081 22 |
| string | SSH_CONNECTION | 10.0.2.3 44081 10.0.2.8 22 |
| string | SSH_TTY | /dev/pts/131 |
| string | STY | 7366.pts-131.kali |
| string | system | local |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#57:co#205:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{||}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:*4=\\E[3;2~:\\\n\t:*7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km: |
| int | timeout | -1 |
| string | USER | annashch |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/annashch/av_scripts |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1091 |
| string | XDG_SESSION_ID | 897 |