| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
| Num | 1 | | ID | task.align_bowtie2.bowtie2_PE_rep2.line_133.id_7 | | Name | bowtie2_PE rep2 | | Thread | thread_21 | | PID | 130054 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-16 20:16:36 | | End | 2016-05-17 05:25:05 | | Elapsed | 09:08:28 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair2.trim.fastq.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.align.log
| | Dependencies | | |
# SYS command. line 135
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 139
bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 95 files...
|
| Num | 2 | | ID | task.align_bowtie2.bowtie2_PE_rep1.line_133.id_6 | | Name | bowtie2_PE rep1 | | Thread | thread_20 | | PID | 130059 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-16 20:16:36 | | End | 2016-05-17 08:31:13 | | Elapsed | 12:14:36 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair2.trim.fastq.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.align.log
| | Dependencies | | |
# SYS command. line 135
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 139
bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 135 files...
|
| Num | 3 | | ID | task.postalign_bam.dedup_bam_PE_rep2.line_215.id_8 | | Name | dedup_bam_PE rep2 | | Thread | thread_21 | | PID | 9814 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 05:25:06 | | End | 2016-05-17 08:02:20 | | Elapsed | 02:37:14 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
| | Dependencies | | |
# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
echo
# SYS command. line 229
samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark
# SYS command. line 230
echo
# SYS command. line 237
samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 243
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 244
export MAX_JAVA_MEM="12G"
# SYS command. line 247
if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam
--------------------Stdout--------------------
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 62 files...
[bam_sort_core] merging from 62 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 06:50:01 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue May 17 06:50:01 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-05-17 06:50:01 MarkDuplicates Start of doWork freeMemory: 254889800; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-05-17 06:50:01 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-05-17 06:50:01 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-05-17 06:50:18 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr10:105,471,941
INFO 2016-05-17 06:50:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:50:27 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 9s. Last read position: chr11:61,189,008
INFO 2016-05-17 06:50:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:50:43 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 15s. Last read position: chr12:7,527,275
INFO 2016-05-17 06:50:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:50:50 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 7s. Last read position: chr12:120,904,998
INFO 2016-05-17 06:50:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:50:59 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 8s. Last read position: chr14:25,363,911
INFO 2016-05-17 06:50:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:51:03 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 4s. Last read position: chr15:45,459,571
INFO 2016-05-17 06:51:03 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-05-17 06:51:11 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 7s. Last read position: chr16:29,690,354
INFO 2016-05-17 06:51:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-05-17 06:51:16 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 5s. Last read position: chr17:22,020,698
INFO 2016-05-17 06:51:16 MarkDuplicates Tracking 596 as yet unmatched pairs. 596 records in RAM.
INFO 2016-05-17 06:51:24 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 8s. Last read position: chr18:22,716,980
INFO 2016-05-17 06:51:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:51:29 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 4s. Last read position: chr19:36,273,964
INFO 2016-05-17 06:51:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:51:38 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 9s. Last read position: chr1:20,208,920
INFO 2016-05-17 06:51:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:51:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 5s. Last read position: chr1:113,689,537
INFO 2016-05-17 06:51:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-05-17 06:51:50 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 6s. Last read position: chr1:234,214,540
INFO 2016-05-17 06:51:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:02 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 11s. Last read position: chr21:32,190,981
INFO 2016-05-17 06:52:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:21 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 18s. Last read position: chr2:26,215,748
INFO 2016-05-17 06:52:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:27 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: chr2:141,162,119
INFO 2016-05-17 06:52:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:32 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 4s. Last read position: chr3:9,238,711
INFO 2016-05-17 06:52:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 4s. Last read position: chr3:119,813,196
INFO 2016-05-17 06:52:36 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-05-17 06:52:43 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 6s. Last read position: chr4:20,910,363
INFO 2016-05-17 06:52:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:52:48 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 5s. Last read position: chr4:160,236,142
INFO 2016-05-17 06:52:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:52:54 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 6s. Last read position: chr5:99,830,506
INFO 2016-05-17 06:52:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:53:01 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 7s. Last read position: chr5:170,108,034
INFO 2016-05-17 06:53:01 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:53:06 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 5s. Last read position: chr6:98,393,285
INFO 2016-05-17 06:53:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:53:12 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 5s. Last read position: chr7:35,590,535
INFO 2016-05-17 06:53:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:53:20 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 7s. Last read position: chr7:150,715,716
INFO 2016-05-17 06:53:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-05-17 06:53:26 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 6s. Last read position: chr8:101,734,947
INFO 2016-05-17 06:53:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:53:32 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 6s. Last read position: chr9:92,479,921
INFO 2016-05-17 06:53:32 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 06:53:41 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 8s. Last read position: chrM:79
INFO 2016-05-17 06:53:41 MarkDuplicates Tracking 18882 as yet unmatched pairs. 18882 records in RAM.
INFO 2016-05-17 06:53:46 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 5s. Last read position: chrM:442
INFO 2016-05-17 06:53:46 MarkDuplicates Tracking 8188 as yet unmatched pairs. 8188 records in RAM.
INFO 2016-05-17 06:53:59 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 12s. Last read position: chrM:566
INFO 2016-05-17 06:53:59 MarkDuplicates Tracking 12920 as yet unmatched pairs. 12920 records in RAM.
INFO 2016-05-17 06:54:05 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 6s. Last read position: chrM:770
INFO 2016-05-17 06:54:05 MarkDuplicates Tracking 9282 as yet unmatched pairs. 9282 records in RAM.
INFO 2016-05-17 06:54:09 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 3s. Last read position: chrM:1,224
INFO 2016-05-17 06:54:09 MarkDuplicates Tracking 7360 as yet unmatched pairs. 7360 records in RAM.
INFO 2016-05-17 06:54:12 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 3s. Last read position: chrM:1,466
INFO 2016-05-17 06:54:12 MarkDuplicates Tracking 8074 as yet unmatched pairs. 8074 records in RAM.
INFO 2016-05-17 06:54:15 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 3s. Last read position: chrM:1,742
INFO 2016-05-17 06:54:15 MarkDuplicates Tracking 3620 as yet unmatched pairs. 3620 records in RAM.
INFO 2016-05-17 06:54:20 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 4s. Last read position: chrM:2,166
INFO 2016-05-17 06:54:20 MarkDuplicates Tracking 10712 as yet unmatched pairs. 10712 records in RAM.
INFO 2016-05-17 06:54:25 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 5s. Last read position: chrM:2,555
INFO 2016-05-17 06:54:25 MarkDuplicates Tracking 11520 as yet unmatched pairs. 11520 records in RAM.
INFO 2016-05-17 06:54:32 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 6s. Last read position: chrM:2,728
INFO 2016-05-17 06:54:32 MarkDuplicates Tracking 37906 as yet unmatched pairs. 37906 records in RAM.
INFO 2016-05-17 06:54:40 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 8s. Last read position: chrM:2,933
INFO 2016-05-17 06:54:40 MarkDuplicates Tracking 23878 as yet unmatched pairs. 23878 records in RAM.
INFO 2016-05-17 06:54:44 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 4s. Last read position: chrM:3,136
INFO 2016-05-17 06:54:44 MarkDuplicates Tracking 30288 as yet unmatched pairs. 30288 records in RAM.
INFO 2016-05-17 06:54:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 5s. Last read position: chrM:3,331
INFO 2016-05-17 06:54:50 MarkDuplicates Tracking 29770 as yet unmatched pairs. 29770 records in RAM.
INFO 2016-05-17 06:54:56 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 5s. Last read position: chrM:3,443
INFO 2016-05-17 06:54:56 MarkDuplicates Tracking 46616 as yet unmatched pairs. 46616 records in RAM.
INFO 2016-05-17 06:55:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 7s. Last read position: chrM:3,574
INFO 2016-05-17 06:55:03 MarkDuplicates Tracking 64880 as yet unmatched pairs. 64880 records in RAM.
INFO 2016-05-17 06:55:10 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 6s. Last read position: chrM:3,689
INFO 2016-05-17 06:55:10 MarkDuplicates Tracking 22172 as yet unmatched pairs. 22172 records in RAM.
INFO 2016-05-17 06:55:16 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 6s. Last read position: chrM:3,873
INFO 2016-05-17 06:55:16 MarkDuplicates Tracking 39912 as yet unmatched pairs. 39912 records in RAM.
INFO 2016-05-17 06:55:26 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 9s. Last read position: chrM:4,299
INFO 2016-05-17 06:55:26 MarkDuplicates Tracking 11596 as yet unmatched pairs. 11596 records in RAM.
INFO 2016-05-17 06:55:32 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 5s. Last read position: chrM:4,914
INFO 2016-05-17 06:55:32 MarkDuplicates Tracking 23536 as yet unmatched pairs. 23536 records in RAM.
INFO 2016-05-17 06:55:35 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 3s. Last read position: chrM:5,312
INFO 2016-05-17 06:55:35 MarkDuplicates Tracking 17680 as yet unmatched pairs. 17680 records in RAM.
INFO 2016-05-17 06:55:37 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chrM:5,775
INFO 2016-05-17 06:55:37 MarkDuplicates Tracking 11406 as yet unmatched pairs. 11406 records in RAM.
INFO 2016-05-17 06:55:41 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 3s. Last read position: chrM:6,230
INFO 2016-05-17 06:55:41 MarkDuplicates Tracking 43434 as yet unmatched pairs. 43434 records in RAM.
INFO 2016-05-17 06:55:46 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 5s. Last read position: chrM:6,360
INFO 2016-05-17 06:55:46 MarkDuplicates Tracking 15004 as yet unmatched pairs. 15004 records in RAM.
INFO 2016-05-17 06:55:50 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 4s. Last read position: chrM:6,522
INFO 2016-05-17 06:55:50 MarkDuplicates Tracking 25526 as yet unmatched pairs. 25526 records in RAM.
INFO 2016-05-17 06:55:55 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 5s. Last read position: chrM:6,898
INFO 2016-05-17 06:55:55 MarkDuplicates Tracking 7018 as yet unmatched pairs. 7018 records in RAM.
INFO 2016-05-17 06:56:01 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 5s. Last read position: chrM:7,234
INFO 2016-05-17 06:56:01 MarkDuplicates Tracking 14370 as yet unmatched pairs. 14370 records in RAM.
INFO 2016-05-17 06:56:09 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 8s. Last read position: chrM:7,820
INFO 2016-05-17 06:56:09 MarkDuplicates Tracking 10836 as yet unmatched pairs. 10836 records in RAM.
INFO 2016-05-17 06:56:14 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 4s. Last read position: chrM:8,061
INFO 2016-05-17 06:56:14 MarkDuplicates Tracking 7248 as yet unmatched pairs. 7248 records in RAM.
INFO 2016-05-17 06:56:19 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 5s. Last read position: chrM:8,417
INFO 2016-05-17 06:56:19 MarkDuplicates Tracking 42818 as yet unmatched pairs. 42818 records in RAM.
INFO 2016-05-17 06:56:24 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 4s. Last read position: chrM:9,036
INFO 2016-05-17 06:56:24 MarkDuplicates Tracking 5808 as yet unmatched pairs. 5808 records in RAM.
INFO 2016-05-17 06:56:29 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 5s. Last read position: chrM:9,296
INFO 2016-05-17 06:56:29 MarkDuplicates Tracking 11026 as yet unmatched pairs. 11026 records in RAM.
INFO 2016-05-17 06:56:52 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 23s. Last read position: chrM:9,739
INFO 2016-05-17 06:56:52 MarkDuplicates Tracking 27778 as yet unmatched pairs. 27778 records in RAM.
INFO 2016-05-17 06:56:56 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chrM:10,046
INFO 2016-05-17 06:56:56 MarkDuplicates Tracking 14690 as yet unmatched pairs. 14690 records in RAM.
INFO 2016-05-17 06:56:59 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 3s. Last read position: chrM:10,335
INFO 2016-05-17 06:56:59 MarkDuplicates Tracking 14658 as yet unmatched pairs. 14658 records in RAM.
INFO 2016-05-17 06:57:02 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 3s. Last read position: chrM:10,653
INFO 2016-05-17 06:57:02 MarkDuplicates Tracking 8034 as yet unmatched pairs. 8034 records in RAM.
INFO 2016-05-17 06:57:07 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 4s. Last read position: chrM:11,114
INFO 2016-05-17 06:57:07 MarkDuplicates Tracking 3052 as yet unmatched pairs. 3052 records in RAM.
INFO 2016-05-17 06:57:12 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 5s. Last read position: chrM:11,308
INFO 2016-05-17 06:57:12 MarkDuplicates Tracking 14464 as yet unmatched pairs. 14464 records in RAM.
INFO 2016-05-17 06:57:15 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chrM:11,556
INFO 2016-05-17 06:57:15 MarkDuplicates Tracking 4934 as yet unmatched pairs. 4934 records in RAM.
INFO 2016-05-17 06:57:18 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chrM:11,937
INFO 2016-05-17 06:57:18 MarkDuplicates Tracking 4940 as yet unmatched pairs. 4940 records in RAM.
INFO 2016-05-17 06:57:21 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 3s. Last read position: chrM:12,096
INFO 2016-05-17 06:57:21 MarkDuplicates Tracking 16982 as yet unmatched pairs. 16982 records in RAM.
INFO 2016-05-17 06:57:26 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 4s. Last read position: chrM:12,427
INFO 2016-05-17 06:57:26 MarkDuplicates Tracking 17514 as yet unmatched pairs. 17514 records in RAM.
INFO 2016-05-17 06:57:30 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 4s. Last read position: chrM:12,621
INFO 2016-05-17 06:57:30 MarkDuplicates Tracking 26964 as yet unmatched pairs. 26964 records in RAM.
INFO 2016-05-17 06:57:36 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 5s. Last read position: chrM:12,969
INFO 2016-05-17 06:57:36 MarkDuplicates Tracking 12264 as yet unmatched pairs. 12264 records in RAM.
INFO 2016-05-17 06:57:40 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 4s. Last read position: chrM:13,090
INFO 2016-05-17 06:57:40 MarkDuplicates Tracking 33332 as yet unmatched pairs. 33332 records in RAM.
INFO 2016-05-17 06:57:46 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 5s. Last read position: chrM:13,295
INFO 2016-05-17 06:57:46 MarkDuplicates Tracking 8822 as yet unmatched pairs. 8822 records in RAM.
INFO 2016-05-17 06:57:51 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 5s. Last read position: chrM:13,499
INFO 2016-05-17 06:57:51 MarkDuplicates Tracking 12078 as yet unmatched pairs. 12078 records in RAM.
INFO 2016-05-17 06:58:04 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 12s. Last read position: chrM:13,720
INFO 2016-05-17 06:58:04 MarkDuplicates Tracking 11678 as yet unmatched pairs. 11678 records in RAM.
INFO 2016-05-17 06:58:09 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 4s. Last read position: chrM:13,954
INFO 2016-05-17 06:58:09 MarkDuplicates Tracking 26764 as yet unmatched pairs. 26764 records in RAM.
INFO 2016-05-17 06:58:14 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 4s. Last read position: chrM:14,276
INFO 2016-05-17 06:58:14 MarkDuplicates Tracking 14258 as yet unmatched pairs. 14258 records in RAM.
INFO 2016-05-17 06:58:18 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 4s. Last read position: chrM:14,446
INFO 2016-05-17 06:58:18 MarkDuplicates Tracking 4002 as yet unmatched pairs. 4002 records in RAM.
INFO 2016-05-17 06:58:24 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 5s. Last read position: chrM:14,856
INFO 2016-05-17 06:58:24 MarkDuplicates Tracking 9778 as yet unmatched pairs. 9778 records in RAM.
INFO 2016-05-17 06:58:30 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 6s. Last read position: chrM:15,095
INFO 2016-05-17 06:58:30 MarkDuplicates Tracking 12554 as yet unmatched pairs. 12554 records in RAM.
INFO 2016-05-17 06:58:33 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 3s. Last read position: chrM:15,252
INFO 2016-05-17 06:58:33 MarkDuplicates Tracking 14512 as yet unmatched pairs. 14512 records in RAM.
INFO 2016-05-17 06:58:36 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 3s. Last read position: chrM:15,423
INFO 2016-05-17 06:58:36 MarkDuplicates Tracking 29688 as yet unmatched pairs. 29688 records in RAM.
INFO 2016-05-17 06:58:39 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 3s. Last read position: chrM:15,585
INFO 2016-05-17 06:58:39 MarkDuplicates Tracking 27210 as yet unmatched pairs. 27210 records in RAM.
INFO 2016-05-17 06:58:42 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 3s. Last read position: chrM:15,742
INFO 2016-05-17 06:58:42 MarkDuplicates Tracking 28972 as yet unmatched pairs. 28972 records in RAM.
INFO 2016-05-17 06:58:48 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 5s. Last read position: chrM:15,925
INFO 2016-05-17 06:58:48 MarkDuplicates Tracking 20532 as yet unmatched pairs. 20532 records in RAM.
INFO 2016-05-17 06:58:53 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 5s. Last read position: chrM:16,301
INFO 2016-05-17 06:58:53 MarkDuplicates Tracking 15704 as yet unmatched pairs. 15704 records in RAM.
INFO 2016-05-17 06:58:58 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 5s. Last read position: chrM:16,447
INFO 2016-05-17 06:58:58 MarkDuplicates Tracking 5336 as yet unmatched pairs. 5336 records in RAM.
INFO 2016-05-17 06:59:03 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 4s. Last read position: chrX:101,854,260
INFO 2016-05-17 06:59:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 06:59:06 MarkDuplicates Read 87423356 records. 0 pairs never matched.
INFO 2016-05-17 06:59:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 3408266648; totalMemory: 3436183552; maxMemory: 3817865216
INFO 2016-05-17 06:59:17 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk.
INFO 2016-05-17 06:59:17 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-05-17 06:59:55 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-05-17 07:00:15 MarkDuplicates Sorting list of duplicate records.
INFO 2016-05-17 07:00:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 2491402080; totalMemory: 3472883712; maxMemory: 3817865216
INFO 2016-05-17 07:00:19 MarkDuplicates Marking 61271874 records as duplicates.
INFO 2016-05-17 07:00:19 MarkDuplicates Found 28057333 optical duplicate clusters.
INFO 2016-05-17 07:02:01 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 100s. Last read position: chr19:36,273,964
INFO 2016-05-17 07:03:43 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:03:22s. Time for last 10,000,000: 102s. Last read position: chr4:160,236,142
INFO 2016-05-17 07:05:21 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:04:59s. Time for last 10,000,000: 97s. Last read position: chrM:566
INFO 2016-05-17 07:06:39 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:06:18s. Time for last 10,000,000: 78s. Last read position: chrM:3,331
INFO 2016-05-17 07:07:54 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:07:32s. Time for last 10,000,000: 74s. Last read position: chrM:6,360
INFO 2016-05-17 07:09:12 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:08:51s. Time for last 10,000,000: 78s. Last read position: chrM:10,046
INFO 2016-05-17 07:10:28 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:10:07s. Time for last 10,000,000: 75s. Last read position: chrM:12,969
INFO 2016-05-17 07:11:42 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:11:21s. Time for last 10,000,000: 74s. Last read position: chrM:15,252
INFO 2016-05-17 07:12:44 MarkDuplicates Before output close freeMemory: 3521344000; totalMemory: 3551526912; maxMemory: 3817865216
INFO 2016-05-17 07:12:44 MarkDuplicates After output close freeMemory: 3521342944; totalMemory: 3551526912; maxMemory: 3817865216
[Tue May 17 07:12:44 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.71 minutes.
Runtime.totalMemory()=3551526912
[bam_sort_core] merging from 63 files...
|
| Num | 4 | | ID | task.postalign_bam.nmsrt_bam_rep2.line_321.id_9 | | Name | nmsrt_bam rep2 | | Thread | thread_21 | | PID | 40400 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:02:21 | | End | 2016-05-17 08:14:32 | | Elapsed | 00:12:11 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
| | Dependencies | | |
# SYS command. line 323
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 325
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.nmsrt
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 18 files...
|
| Num | 5 | | ID | task.postalign_bam.bam_to_bedpe_rep2.line_425.id_10 | | Name | bam_to_bedpe rep2 | | Thread | thread_21 | | PID | 40743 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:14:33 | | End | 2016-05-17 08:15:56 | | Elapsed | 00:01:23 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Dependencies | nmsrt_bam rep2
nmsrt_bam rep2
| |
# SYS command. line 427
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 430
bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 6 | | ID | task.postalign_bed.subsample_bedpe_rep2.line_116.id_11 | | Name | subsample_bedpe rep2 | | Thread | thread_21 | | PID | 40824 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:15:57 | | End | 2016-05-17 08:17:18 | | Elapsed | 00:01:21 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
| | Dependencies | | |
# SYS command. line 118
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 120
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 7 | | ID | task.postalign_bam.bedpe_to_tag_rep2.line_465.id_12 | | Name | bedpe_to_tag rep2 | | Thread | thread_21 | | PID | 40896 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:17:19 | | End | 2016-05-17 08:18:26 | | Elapsed | 00:01:06 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
| | Dependencies | | |
# SYS command. line 467
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 469
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
# SYS command. line 472
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 8 | | ID | task.postalign_bed.shift_tag_rep2.line_140.id_13 | | Name | shift_tag rep2 | | Thread | thread_21 | | PID | 40967 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:18:27 | | End | 2016-05-17 08:19:05 | | Elapsed | 00:00:38 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Dependencies | | |
# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 9 | | ID | task.postalign_bed.subsample_bedpe2tagrep2.line_89.id_14 | | Name | subsample_bedpe2tagrep2 | | Thread | thread_21 | | PID | 41033 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:19:06 | | End | 2016-05-17 08:20:00 | | Elapsed | 00:00:54 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
| | Dependencies | | |
# SYS command. line 91
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
grep -v "chrM" | shuf -n 25000000 | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 10 | | ID | task.postalign_bed.xcor_rep2.line_165.id_15 | | Name | xcor rep2 | | Thread | thread_21 | | PID | 41165 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:20:01 | | End | 2016-05-17 08:36:38 | | Elapsed | 00:16:36 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
| | Dependencies | | |
# SYS command. line 167
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 171
Rscript $(which run_spp_nodups.R) -rf \
-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0
# SYS command. line 174
sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp
# SYS command. line 175
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 0
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
opened /tmp/RtmpkUFBdx/ATAC16-trimmed-pair1.trim.PE2SE.nodup.25.tagAligna176129dbe53
done. read 12075155 fragments
ChIP data read length 63
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1225169
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.21547695385749
Top 3 estimates for fragment length 0
Window half size 375
Phantom peak location 55
Phantom peak Correlation 0.2322179
Normalized Strand cross-correlation coefficient (NSC) 1.758752
Relative Strand Cross correlation Coefficient (RSC) 0.847395
Phantom Peak Quality Tag 0
null device
1
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools
|
| Num | 11 | | ID | task.callpeak_macs2.macs2_atac_rep2.pval0.1.line_192.id_16 | | Name | macs2_atac rep2.pval0.1 | | Thread | thread_21 | | PID | 41175 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 08:20:01 | | End | 2016-05-17 08:32:48 | | Elapsed | 00:12:47 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 08:20:04:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 08:20:04: #1 read tag files...
INFO @ Tue, 17 May 2016 08:20:04: #1 read treatment tags...
INFO @ Tue, 17 May 2016 08:20:06: 1000000
INFO @ Tue, 17 May 2016 08:20:07: 2000000
INFO @ Tue, 17 May 2016 08:20:09: 3000000
INFO @ Tue, 17 May 2016 08:20:11: 4000000
INFO @ Tue, 17 May 2016 08:20:13: 5000000
INFO @ Tue, 17 May 2016 08:20:14: 6000000
INFO @ Tue, 17 May 2016 08:20:16: 7000000
INFO @ Tue, 17 May 2016 08:20:18: 8000000
INFO @ Tue, 17 May 2016 08:20:19: 9000000
INFO @ Tue, 17 May 2016 08:20:21: 10000000
INFO @ Tue, 17 May 2016 08:20:22: 11000000
INFO @ Tue, 17 May 2016 08:20:24: 12000000
INFO @ Tue, 17 May 2016 08:20:26: 13000000
INFO @ Tue, 17 May 2016 08:20:27: 14000000
INFO @ Tue, 17 May 2016 08:20:29: 15000000
INFO @ Tue, 17 May 2016 08:20:31: 16000000
INFO @ Tue, 17 May 2016 08:20:32: 17000000
INFO @ Tue, 17 May 2016 08:20:34: 18000000
INFO @ Tue, 17 May 2016 08:20:36: 19000000
INFO @ Tue, 17 May 2016 08:20:37: 20000000
INFO @ Tue, 17 May 2016 08:20:39: 21000000
INFO @ Tue, 17 May 2016 08:20:41: 22000000
INFO @ Tue, 17 May 2016 08:20:42: 23000000
INFO @ Tue, 17 May 2016 08:20:44: 24000000
INFO @ Tue, 17 May 2016 08:20:46: #1 tag size is determined as 81 bps
INFO @ Tue, 17 May 2016 08:20:46: #1 tag size = 81
INFO @ Tue, 17 May 2016 08:20:46: #1 total tags in treatment: 24150310
INFO @ Tue, 17 May 2016 08:20:46: #1 finished!
INFO @ Tue, 17 May 2016 08:20:46: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 08:20:46: #2 Skipped...
INFO @ Tue, 17 May 2016 08:20:46: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 08:20:46: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 08:20:46: #3 Call peaks...
INFO @ Tue, 17 May 2016 08:20:46: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000...
INFO @ Tue, 17 May 2016 08:20:46: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 08:22:01: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 08:23:55: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 08:23:58: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak
INFO @ Tue, 17 May 2016 08:24:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak
INFO @ Tue, 17 May 2016 08:24:03: Done!
INFO @ Tue, 17 May 2016 08:24:19:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 08:24:19: #1 read tag files...
INFO @ Tue, 17 May 2016 08:24:19: #1 read treatment tags...
INFO @ Tue, 17 May 2016 08:24:21: 1000000
INFO @ Tue, 17 May 2016 08:24:23: 2000000
INFO @ Tue, 17 May 2016 08:24:25: 3000000
INFO @ Tue, 17 May 2016 08:24:26: 4000000
INFO @ Tue, 17 May 2016 08:24:28: 5000000
INFO @ Tue, 17 May 2016 08:24:29: 6000000
INFO @ Tue, 17 May 2016 08:24:31: 7000000
INFO @ Tue, 17 May 2016 08:24:33: 8000000
INFO @ Tue, 17 May 2016 08:24:34: 9000000
INFO @ Tue, 17 May 2016 08:24:36: 10000000
INFO @ Tue, 17 May 2016 08:24:38: 11000000
INFO @ Tue, 17 May 2016 08:24:39: 12000000
INFO @ Tue, 17 May 2016 08:24:41: 13000000
INFO @ Tue, 17 May 2016 08:24:42: 14000000
INFO @ Tue, 17 May 2016 08:24:44: 15000000
INFO @ Tue, 17 May 2016 08:24:46: 16000000
INFO @ Tue, 17 May 2016 08:24:47: 17000000
INFO @ Tue, 17 May 2016 08:24:49: 18000000
INFO @ Tue, 17 May 2016 08:24:51: 19000000
INFO @ Tue, 17 May 2016 08:24:52: 20000000
INFO @ Tue, 17 May 2016 08:24:54: 21000000
INFO @ Tue, 17 May 2016 08:24:55: 22000000
INFO @ Tue, 17 May 2016 08:24:57: 23000000
INFO @ Tue, 17 May 2016 08:24:59: 24000000
INFO @ Tue, 17 May 2016 08:25:01: #1 tag size is determined as 81 bps
INFO @ Tue, 17 May 2016 08:25:01: #1 tag size = 81
INFO @ Tue, 17 May 2016 08:25:01: #1 total tags in treatment: 24150310
INFO @ Tue, 17 May 2016 08:25:01: #1 finished!
INFO @ Tue, 17 May 2016 08:25:01: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 08:25:01: #2 Skipped...
INFO @ Tue, 17 May 2016 08:25:01: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 08:25:01: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 08:25:01: #3 Call peaks...
INFO @ Tue, 17 May 2016 08:25:01: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 08:25:01: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ...
INFO @ Tue, 17 May 2016 08:25:01: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 08:25:58: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 08:25:58: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg
INFO @ Tue, 17 May 2016 08:25:58: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg
INFO @ Tue, 17 May 2016 08:25:58: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 08:25:58: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 08:32:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 08:32:35: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak
INFO @ Tue, 17 May 2016 08:32:39: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed
INFO @ Tue, 17 May 2016 08:32:41: Done!
|
| Num | 12 | | ID | task.callpeak_macs2.macs2_atac_rep2.line_192.id_17 | | Name | macs2_atac rep2 | | Thread | thread_21 | | PID | 41190 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 08:20:01 | | End | 2016-05-17 08:49:01 | | Elapsed | 00:28:59 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 08:20:04:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 08:20:04: #1 read tag files...
INFO @ Tue, 17 May 2016 08:20:04: #1 read treatment tags...
INFO @ Tue, 17 May 2016 08:20:06: 1000000
INFO @ Tue, 17 May 2016 08:20:07: 2000000
INFO @ Tue, 17 May 2016 08:20:09: 3000000
INFO @ Tue, 17 May 2016 08:20:11: 4000000
INFO @ Tue, 17 May 2016 08:20:12: 5000000
INFO @ Tue, 17 May 2016 08:20:14: 6000000
INFO @ Tue, 17 May 2016 08:20:16: 7000000
INFO @ Tue, 17 May 2016 08:20:18: 8000000
INFO @ Tue, 17 May 2016 08:20:19: 9000000
INFO @ Tue, 17 May 2016 08:20:21: 10000000
INFO @ Tue, 17 May 2016 08:20:23: 11000000
INFO @ Tue, 17 May 2016 08:20:25: 12000000
INFO @ Tue, 17 May 2016 08:20:26: 13000000
INFO @ Tue, 17 May 2016 08:20:28: 14000000
INFO @ Tue, 17 May 2016 08:20:29: 15000000
INFO @ Tue, 17 May 2016 08:20:31: 16000000
INFO @ Tue, 17 May 2016 08:20:33: 17000000
INFO @ Tue, 17 May 2016 08:20:34: 18000000
INFO @ Tue, 17 May 2016 08:20:36: 19000000
INFO @ Tue, 17 May 2016 08:20:38: 20000000
INFO @ Tue, 17 May 2016 08:20:39: 21000000
INFO @ Tue, 17 May 2016 08:20:41: 22000000
INFO @ Tue, 17 May 2016 08:20:42: 23000000
INFO @ Tue, 17 May 2016 08:20:44: 24000000
INFO @ Tue, 17 May 2016 08:20:46: #1 tag size is determined as 81 bps
INFO @ Tue, 17 May 2016 08:20:46: #1 tag size = 81
INFO @ Tue, 17 May 2016 08:20:46: #1 total tags in treatment: 24150310
INFO @ Tue, 17 May 2016 08:20:46: #1 finished!
INFO @ Tue, 17 May 2016 08:20:46: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 08:20:46: #2 Skipped...
INFO @ Tue, 17 May 2016 08:20:46: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 08:20:46: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 08:20:46: #3 Call peaks...
INFO @ Tue, 17 May 2016 08:20:46: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Tue, 17 May 2016 08:20:46: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 08:21:57: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 08:23:25: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls
INFO @ Tue, 17 May 2016 08:23:28: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak
INFO @ Tue, 17 May 2016 08:23:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak
INFO @ Tue, 17 May 2016 08:23:32: Done!
INFO @ Tue, 17 May 2016 08:23:44:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 08:23:44: #1 read tag files...
INFO @ Tue, 17 May 2016 08:23:44: #1 read treatment tags...
INFO @ Tue, 17 May 2016 08:23:45: 1000000
INFO @ Tue, 17 May 2016 08:23:47: 2000000
INFO @ Tue, 17 May 2016 08:23:49: 3000000
INFO @ Tue, 17 May 2016 08:23:51: 4000000
INFO @ Tue, 17 May 2016 08:23:52: 5000000
INFO @ Tue, 17 May 2016 08:23:54: 6000000
INFO @ Tue, 17 May 2016 08:23:56: 7000000
INFO @ Tue, 17 May 2016 08:23:58: 8000000
INFO @ Tue, 17 May 2016 08:23:59: 9000000
INFO @ Tue, 17 May 2016 08:24:01: 10000000
INFO @ Tue, 17 May 2016 08:24:03: 11000000
INFO @ Tue, 17 May 2016 08:24:05: 12000000
INFO @ Tue, 17 May 2016 08:24:07: 13000000
INFO @ Tue, 17 May 2016 08:24:08: 14000000
INFO @ Tue, 17 May 2016 08:24:10: 15000000
INFO @ Tue, 17 May 2016 08:24:12: 16000000
INFO @ Tue, 17 May 2016 08:24:14: 17000000
INFO @ Tue, 17 May 2016 08:24:15: 18000000
INFO @ Tue, 17 May 2016 08:24:17: 19000000
INFO @ Tue, 17 May 2016 08:24:19: 20000000
INFO @ Tue, 17 May 2016 08:24:20: 21000000
INFO @ Tue, 17 May 2016 08:24:23: 22000000
INFO @ Tue, 17 May 2016 08:24:24: 23000000
INFO @ Tue, 17 May 2016 08:24:26: 24000000
INFO @ Tue, 17 May 2016 08:24:28: #1 tag size is determined as 81 bps
INFO @ Tue, 17 May 2016 08:24:28: #1 tag size = 81
INFO @ Tue, 17 May 2016 08:24:28: #1 total tags in treatment: 24150310
INFO @ Tue, 17 May 2016 08:24:28: #1 finished!
INFO @ Tue, 17 May 2016 08:24:28: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 08:24:28: #2 Skipped...
INFO @ Tue, 17 May 2016 08:24:28: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 08:24:28: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 08:24:28: #3 Call peaks...
INFO @ Tue, 17 May 2016 08:24:28: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 08:24:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Tue, 17 May 2016 08:24:28: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 08:25:20: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 08:25:20: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg
INFO @ Tue, 17 May 2016 08:25:20: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg
INFO @ Tue, 17 May 2016 08:25:20: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 08:25:20: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 08:29:21: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls
INFO @ Tue, 17 May 2016 08:29:23: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak
INFO @ Tue, 17 May 2016 08:29:24: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed
INFO @ Tue, 17 May 2016 08:29:25: Done!
INFO @ Tue, 17 May 2016 08:29:28: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 08:30:13: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 08:30:34: Build scoreTrackII...
INFO @ Tue, 17 May 2016 08:30:53: Calculate scores comparing treatment and control by 'FE'...
INFO @ Tue, 17 May 2016 08:33:22: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 08:34:47: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'!
INFO @ Tue, 17 May 2016 08:39:20: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 08:40:02: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 08:40:22: Build scoreTrackII...
INFO @ Tue, 17 May 2016 08:40:50: Values in your input bedGraph files will be multiplied by 24.150310 ...
INFO @ Tue, 17 May 2016 08:43:14: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Tue, 17 May 2016 08:43:34: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 08:44:57: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!
|
| Num | 13 | | ID | task.postalign_bam.dedup_bam_PE_rep1.line_215.id_18 | | Name | dedup_bam_PE rep1 | | Thread | thread_20 | | PID | 41574 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 08:31:14 | | End | 2016-05-17 12:35:02 | | Elapsed | 04:03:48 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
| | Dependencies | | |
# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
echo
# SYS command. line 229
samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark
# SYS command. line 230
echo
# SYS command. line 237
samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 243
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 244
export MAX_JAVA_MEM="12G"
# SYS command. line 247
if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam
--------------------Stdout--------------------
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 88 files...
[bam_sort_core] merging from 88 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Tue May 17 10:31:10 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue May 17 10:31:10 PDT 2016] Executing as pangwei@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-05-17 10:31:10 MarkDuplicates Start of doWork freeMemory: 254889768; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-05-17 10:31:10 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-05-17 10:31:10 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-05-17 10:31:20 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr10:80,938,486
INFO 2016-05-17 10:31:20 MarkDuplicates Tracking 24 as yet unmatched pairs. 24 records in RAM.
INFO 2016-05-17 10:31:29 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 8s. Last read position: chr11:2,027,612
INFO 2016-05-17 10:31:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:31:33 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 4s. Last read position: chr11:67,188,403
INFO 2016-05-17 10:31:33 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-05-17 10:31:38 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 5s. Last read position: chr11:132,728,302
INFO 2016-05-17 10:31:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:31:44 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 6s. Last read position: chr12:72,506,264
INFO 2016-05-17 10:31:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:31:52 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 7s. Last read position: chr13:31,254,042
INFO 2016-05-17 10:31:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:31:57 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 5s. Last read position: chr14:24,658,087
INFO 2016-05-17 10:31:57 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-05-17 10:32:04 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 6s. Last read position: chr14:101,137,366
INFO 2016-05-17 10:32:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:32:10 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 6s. Last read position: chr15:81,616,414
INFO 2016-05-17 10:32:10 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-05-17 10:32:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 11s. Last read position: chr16:55,764,373
INFO 2016-05-17 10:32:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:32:28 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 6s. Last read position: chr17:13,505,464
INFO 2016-05-17 10:32:28 MarkDuplicates Tracking 26 as yet unmatched pairs. 26 records in RAM.
INFO 2016-05-17 10:32:36 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 7s. Last read position: chr17:72,740,434
INFO 2016-05-17 10:32:36 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:32:47 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 10s. Last read position: chr18:60,254,230
INFO 2016-05-17 10:32:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:32:55 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 8s. Last read position: chr19:39,799,122
INFO 2016-05-17 10:32:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-05-17 10:33:18 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 22s. Last read position: chr1:3,673,099
INFO 2016-05-17 10:33:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:33:28 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 9s. Last read position: chr1:54,794,483
INFO 2016-05-17 10:33:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:33:35 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 7s. Last read position: chr1:156,082,582
INFO 2016-05-17 10:33:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:33:43 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 7s. Last read position: chr1:226,384,929
INFO 2016-05-17 10:33:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:33:52 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 9s. Last read position: chr20:44,446,014
INFO 2016-05-17 10:33:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:33:59 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 6s. Last read position: chr22:28,614,815
INFO 2016-05-17 10:33:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:34:08 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 8s. Last read position: chr2:34,757,709
INFO 2016-05-17 10:34:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:34:21 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 12s. Last read position: chr2:121,141,672
INFO 2016-05-17 10:34:21 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-05-17 10:34:29 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 7s. Last read position: chr2:206,641,707
INFO 2016-05-17 10:34:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:34:38 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 9s. Last read position: chr3:30,867,065
INFO 2016-05-17 10:34:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:34:47 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 8s. Last read position: chr3:113,014,381
INFO 2016-05-17 10:34:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:35:00 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 13s. Last read position: chr3:189,058,796
INFO 2016-05-17 10:35:00 MarkDuplicates Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO 2016-05-17 10:35:07 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 7s. Last read position: chr4:76,364,939
INFO 2016-05-17 10:35:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:35:14 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 7s. Last read position: chr4:170,034,929
INFO 2016-05-17 10:35:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:35:23 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 8s. Last read position: chr5:71,426,202
INFO 2016-05-17 10:35:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:35:47 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 24s. Last read position: chr5:134,262,729
INFO 2016-05-17 10:35:47 MarkDuplicates Tracking 1484 as yet unmatched pairs. 1484 records in RAM.
INFO 2016-05-17 10:35:55 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 7s. Last read position: chr6:3,403,651
INFO 2016-05-17 10:35:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:36:01 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 6s. Last read position: chr6:85,344,886
INFO 2016-05-17 10:36:01 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:36:08 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 6s. Last read position: chr6:168,925,575
INFO 2016-05-17 10:36:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:36:15 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 6s. Last read position: chr7:77,428,482
INFO 2016-05-17 10:36:15 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-05-17 10:36:23 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 8s. Last read position: chr7:152,457,264
INFO 2016-05-17 10:36:23 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-05-17 10:36:31 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 7s. Last read position: chr8:72,129,288
INFO 2016-05-17 10:36:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:36:39 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 8s. Last read position: chr8:145,137,554
INFO 2016-05-17 10:36:39 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-05-17 10:36:47 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 8s. Last read position: chr9:110,099,186
INFO 2016-05-17 10:36:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-05-17 10:36:59 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 11s. Last read position: chrM:42
INFO 2016-05-17 10:36:59 MarkDuplicates Tracking 23068 as yet unmatched pairs. 23068 records in RAM.
INFO 2016-05-17 10:37:06 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 6s. Last read position: chrM:333
INFO 2016-05-17 10:37:06 MarkDuplicates Tracking 30342 as yet unmatched pairs. 30342 records in RAM.
INFO 2016-05-17 10:37:13 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 7s. Last read position: chrM:486
INFO 2016-05-17 10:37:13 MarkDuplicates Tracking 25478 as yet unmatched pairs. 25478 records in RAM.
INFO 2016-05-17 10:37:21 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 7s. Last read position: chrM:560
INFO 2016-05-17 10:37:21 MarkDuplicates Tracking 37358 as yet unmatched pairs. 37358 records in RAM.
INFO 2016-05-17 10:37:28 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 7s. Last read position: chrM:712
INFO 2016-05-17 10:37:28 MarkDuplicates Tracking 29304 as yet unmatched pairs. 29304 records in RAM.
INFO 2016-05-17 10:37:40 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 11s. Last read position: chrM:858
INFO 2016-05-17 10:37:40 MarkDuplicates Tracking 22008 as yet unmatched pairs. 22008 records in RAM.
INFO 2016-05-17 10:37:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 15s. Last read position: chrM:1,239
INFO 2016-05-17 10:37:55 MarkDuplicates Tracking 9250 as yet unmatched pairs. 9250 records in RAM.
INFO 2016-05-17 10:38:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 8s. Last read position: chrM:1,387
INFO 2016-05-17 10:38:04 MarkDuplicates Tracking 11792 as yet unmatched pairs. 11792 records in RAM.
INFO 2016-05-17 10:38:10 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 6s. Last read position: chrM:1,573
INFO 2016-05-17 10:38:10 MarkDuplicates Tracking 9256 as yet unmatched pairs. 9256 records in RAM.
INFO 2016-05-17 10:38:19 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 8s. Last read position: chrM:1,832
INFO 2016-05-17 10:38:19 MarkDuplicates Tracking 5688 as yet unmatched pairs. 5688 records in RAM.
INFO 2016-05-17 10:38:31 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 12s. Last read position: chrM:2,063
INFO 2016-05-17 10:38:31 MarkDuplicates Tracking 13578 as yet unmatched pairs. 13578 records in RAM.
INFO 2016-05-17 10:38:37 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 5s. Last read position: chrM:2,380
INFO 2016-05-17 10:38:37 MarkDuplicates Tracking 5062 as yet unmatched pairs. 5062 records in RAM.
INFO 2016-05-17 10:38:43 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 5s. Last read position: chrM:2,585
INFO 2016-05-17 10:38:43 MarkDuplicates Tracking 22648 as yet unmatched pairs. 22648 records in RAM.
INFO 2016-05-17 10:38:48 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 5s. Last read position: chrM:2,708
INFO 2016-05-17 10:38:48 MarkDuplicates Tracking 44530 as yet unmatched pairs. 44530 records in RAM.
INFO 2016-05-17 10:38:52 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chrM:2,851
INFO 2016-05-17 10:38:52 MarkDuplicates Tracking 75866 as yet unmatched pairs. 75866 records in RAM.
INFO 2016-05-17 10:38:59 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 7s. Last read position: chrM:2,980
INFO 2016-05-17 10:38:59 MarkDuplicates Tracking 36904 as yet unmatched pairs. 36904 records in RAM.
INFO 2016-05-17 10:39:07 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 7s. Last read position: chrM:3,122
INFO 2016-05-17 10:39:07 MarkDuplicates Tracking 39900 as yet unmatched pairs. 39900 records in RAM.
INFO 2016-05-17 10:39:13 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 6s. Last read position: chrM:3,285
INFO 2016-05-17 10:39:13 MarkDuplicates Tracking 23924 as yet unmatched pairs. 23924 records in RAM.
INFO 2016-05-17 10:39:21 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 7s. Last read position: chrM:3,368
INFO 2016-05-17 10:39:21 MarkDuplicates Tracking 32466 as yet unmatched pairs. 32466 records in RAM.
INFO 2016-05-17 10:39:29 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 7s. Last read position: chrM:3,446
INFO 2016-05-17 10:39:29 MarkDuplicates Tracking 24992 as yet unmatched pairs. 24992 records in RAM.
INFO 2016-05-17 10:39:47 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 18s. Last read position: chrM:3,535
INFO 2016-05-17 10:39:47 MarkDuplicates Tracking 26216 as yet unmatched pairs. 26216 records in RAM.
INFO 2016-05-17 10:39:52 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 4s. Last read position: chrM:3,616
INFO 2016-05-17 10:39:52 MarkDuplicates Tracking 48124 as yet unmatched pairs. 48124 records in RAM.
INFO 2016-05-17 10:39:58 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 6s. Last read position: chrM:3,705
INFO 2016-05-17 10:39:58 MarkDuplicates Tracking 33826 as yet unmatched pairs. 33826 records in RAM.
INFO 2016-05-17 10:40:03 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 4s. Last read position: chrM:3,838
INFO 2016-05-17 10:40:03 MarkDuplicates Tracking 45624 as yet unmatched pairs. 45624 records in RAM.
INFO 2016-05-17 10:40:10 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 6s. Last read position: chrM:4,044
INFO 2016-05-17 10:40:10 MarkDuplicates Tracking 13322 as yet unmatched pairs. 13322 records in RAM.
INFO 2016-05-17 10:40:15 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 5s. Last read position: chrM:4,430
INFO 2016-05-17 10:40:15 MarkDuplicates Tracking 25702 as yet unmatched pairs. 25702 records in RAM.
INFO 2016-05-17 10:40:21 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 5s. Last read position: chrM:4,897
INFO 2016-05-17 10:40:21 MarkDuplicates Tracking 14268 as yet unmatched pairs. 14268 records in RAM.
INFO 2016-05-17 10:40:26 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 5s. Last read position: chrM:5,090
INFO 2016-05-17 10:40:26 MarkDuplicates Tracking 3454 as yet unmatched pairs. 3454 records in RAM.
INFO 2016-05-17 10:40:35 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 9s. Last read position: chrM:5,369
INFO 2016-05-17 10:40:35 MarkDuplicates Tracking 8420 as yet unmatched pairs. 8420 records in RAM.
INFO 2016-05-17 10:40:42 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 7s. Last read position: chrM:5,796
INFO 2016-05-17 10:40:42 MarkDuplicates Tracking 6032 as yet unmatched pairs. 6032 records in RAM.
INFO 2016-05-17 10:40:50 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 8s. Last read position: chrM:6,200
INFO 2016-05-17 10:40:50 MarkDuplicates Tracking 30860 as yet unmatched pairs. 30860 records in RAM.
INFO 2016-05-17 10:40:58 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 8s. Last read position: chrM:6,278
INFO 2016-05-17 10:40:58 MarkDuplicates Tracking 18320 as yet unmatched pairs. 18320 records in RAM.
INFO 2016-05-17 10:41:07 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 8s. Last read position: chrM:6,377
INFO 2016-05-17 10:41:07 MarkDuplicates Tracking 58542 as yet unmatched pairs. 58542 records in RAM.
INFO 2016-05-17 10:41:15 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 8s. Last read position: chrM:6,491
INFO 2016-05-17 10:41:15 MarkDuplicates Tracking 17760 as yet unmatched pairs. 17760 records in RAM.
INFO 2016-05-17 10:41:27 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 11s. Last read position: chrM:6,613
INFO 2016-05-17 10:41:27 MarkDuplicates Tracking 15138 as yet unmatched pairs. 15138 records in RAM.
INFO 2016-05-17 10:41:41 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 14s. Last read position: chrM:6,984
INFO 2016-05-17 10:41:41 MarkDuplicates Tracking 6598 as yet unmatched pairs. 6598 records in RAM.
INFO 2016-05-17 10:41:48 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 6s. Last read position: chrM:7,228
INFO 2016-05-17 10:41:48 MarkDuplicates Tracking 31952 as yet unmatched pairs. 31952 records in RAM.
INFO 2016-05-17 10:41:56 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 7s. Last read position: chrM:7,767
INFO 2016-05-17 10:41:56 MarkDuplicates Tracking 7134 as yet unmatched pairs. 7134 records in RAM.
INFO 2016-05-17 10:42:02 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 5s. Last read position: chrM:7,868
INFO 2016-05-17 10:42:02 MarkDuplicates Tracking 14448 as yet unmatched pairs. 14448 records in RAM.
INFO 2016-05-17 10:42:08 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 5s. Last read position: chrM:8,076
INFO 2016-05-17 10:42:08 MarkDuplicates Tracking 13904 as yet unmatched pairs. 13904 records in RAM.
INFO 2016-05-17 10:42:15 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 7s. Last read position: chrM:8,352
INFO 2016-05-17 10:42:15 MarkDuplicates Tracking 6872 as yet unmatched pairs. 6872 records in RAM.
INFO 2016-05-17 10:42:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 10s. Last read position: chrM:8,612
INFO 2016-05-17 10:42:25 MarkDuplicates Tracking 16342 as yet unmatched pairs. 16342 records in RAM.
INFO 2016-05-17 10:42:29 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 4s. Last read position: chrM:9,074
INFO 2016-05-17 10:42:29 MarkDuplicates Tracking 9216 as yet unmatched pairs. 9216 records in RAM.
INFO 2016-05-17 10:42:34 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 5s. Last read position: chrM:9,278
INFO 2016-05-17 10:42:34 MarkDuplicates Tracking 3826 as yet unmatched pairs. 3826 records in RAM.
INFO 2016-05-17 10:42:38 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 4s. Last read position: chrM:9,563
INFO 2016-05-17 10:42:38 MarkDuplicates Tracking 7920 as yet unmatched pairs. 7920 records in RAM.
INFO 2016-05-17 10:42:42 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 4s. Last read position: chrM:9,795
INFO 2016-05-17 10:42:42 MarkDuplicates Tracking 36352 as yet unmatched pairs. 36352 records in RAM.
INFO 2016-05-17 10:42:46 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 3s. Last read position: chrM:10,005
INFO 2016-05-17 10:42:46 MarkDuplicates Tracking 36678 as yet unmatched pairs. 36678 records in RAM.
INFO 2016-05-17 10:42:50 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 3s. Last read position: chrM:10,234
INFO 2016-05-17 10:42:50 MarkDuplicates Tracking 27670 as yet unmatched pairs. 27670 records in RAM.
INFO 2016-05-17 10:42:56 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 6s. Last read position: chrM:10,443
INFO 2016-05-17 10:42:56 MarkDuplicates Tracking 4464 as yet unmatched pairs. 4464 records in RAM.
INFO 2016-05-17 10:43:00 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 4s. Last read position: chrM:10,653
INFO 2016-05-17 10:43:00 MarkDuplicates Tracking 22054 as yet unmatched pairs. 22054 records in RAM.
INFO 2016-05-17 10:43:23 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 22s. Last read position: chrM:10,923
INFO 2016-05-17 10:43:23 MarkDuplicates Tracking 2100 as yet unmatched pairs. 2100 records in RAM.
INFO 2016-05-17 10:43:29 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 5s. Last read position: chrM:11,185
INFO 2016-05-17 10:43:29 MarkDuplicates Tracking 16290 as yet unmatched pairs. 16290 records in RAM.
INFO 2016-05-17 10:43:35 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 5s. Last read position: chrM:11,334
INFO 2016-05-17 10:43:35 MarkDuplicates Tracking 2028 as yet unmatched pairs. 2028 records in RAM.
INFO 2016-05-17 10:43:41 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 6s. Last read position: chrM:11,530
INFO 2016-05-17 10:43:41 MarkDuplicates Tracking 4322 as yet unmatched pairs. 4322 records in RAM.
INFO 2016-05-17 10:43:47 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 6s. Last read position: chrM:11,767
INFO 2016-05-17 10:43:47 MarkDuplicates Tracking 5724 as yet unmatched pairs. 5724 records in RAM.
INFO 2016-05-17 10:43:56 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 8s. Last read position: chrM:11,955
INFO 2016-05-17 10:43:56 MarkDuplicates Tracking 13448 as yet unmatched pairs. 13448 records in RAM.
INFO 2016-05-17 10:44:01 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 5s. Last read position: chrM:12,071
INFO 2016-05-17 10:44:01 MarkDuplicates Tracking 20710 as yet unmatched pairs. 20710 records in RAM.
INFO 2016-05-17 10:44:07 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 5s. Last read position: chrM:12,276
INFO 2016-05-17 10:44:07 MarkDuplicates Tracking 2988 as yet unmatched pairs. 2988 records in RAM.
INFO 2016-05-17 10:44:13 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 5s. Last read position: chrM:12,485
INFO 2016-05-17 10:44:13 MarkDuplicates Tracking 18088 as yet unmatched pairs. 18088 records in RAM.
INFO 2016-05-17 10:44:19 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 5s. Last read position: chrM:12,609
INFO 2016-05-17 10:44:19 MarkDuplicates Tracking 35868 as yet unmatched pairs. 35868 records in RAM.
INFO 2016-05-17 10:44:25 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 5s. Last read position: chrM:12,782
INFO 2016-05-17 10:44:25 MarkDuplicates Tracking 3234 as yet unmatched pairs. 3234 records in RAM.
INFO 2016-05-17 10:44:30 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 5s. Last read position: chrM:12,993
INFO 2016-05-17 10:44:30 MarkDuplicates Tracking 4100 as yet unmatched pairs. 4100 records in RAM.
INFO 2016-05-17 10:44:36 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 5s. Last read position: chrM:13,089
INFO 2016-05-17 10:44:36 MarkDuplicates Tracking 41250 as yet unmatched pairs. 41250 records in RAM.
INFO 2016-05-17 10:44:46 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 9s. Last read position: chrM:13,206
INFO 2016-05-17 10:44:46 MarkDuplicates Tracking 48178 as yet unmatched pairs. 48178 records in RAM.
INFO 2016-05-17 10:45:00 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 14s. Last read position: chrM:13,363
INFO 2016-05-17 10:45:00 MarkDuplicates Tracking 24794 as yet unmatched pairs. 24794 records in RAM.
INFO 2016-05-17 10:45:06 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 5s. Last read position: chrM:13,522
INFO 2016-05-17 10:45:06 MarkDuplicates Tracking 12850 as yet unmatched pairs. 12850 records in RAM.
INFO 2016-05-17 10:45:13 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 6s. Last read position: chrM:13,657
INFO 2016-05-17 10:45:13 MarkDuplicates Tracking 38618 as yet unmatched pairs. 38618 records in RAM.
INFO 2016-05-17 10:45:20 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 7s. Last read position: chrM:13,839
INFO 2016-05-17 10:45:20 MarkDuplicates Tracking 46350 as yet unmatched pairs. 46350 records in RAM.
INFO 2016-05-17 10:45:27 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 6s. Last read position: chrM:13,992
INFO 2016-05-17 10:45:27 MarkDuplicates Tracking 54726 as yet unmatched pairs. 54726 records in RAM.
INFO 2016-05-17 10:45:34 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 7s. Last read position: chrM:14,270
INFO 2016-05-17 10:45:34 MarkDuplicates Tracking 24722 as yet unmatched pairs. 24722 records in RAM.
INFO 2016-05-17 10:45:40 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 6s. Last read position: chrM:14,378
INFO 2016-05-17 10:45:40 MarkDuplicates Tracking 18856 as yet unmatched pairs. 18856 records in RAM.
INFO 2016-05-17 10:45:46 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 5s. Last read position: chrM:14,592
INFO 2016-05-17 10:45:46 MarkDuplicates Tracking 7128 as yet unmatched pairs. 7128 records in RAM.
INFO 2016-05-17 10:45:56 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 9s. Last read position: chrM:14,854
INFO 2016-05-17 10:45:56 MarkDuplicates Tracking 17550 as yet unmatched pairs. 17550 records in RAM.
INFO 2016-05-17 10:46:01 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 5s. Last read position: chrM:15,039
INFO 2016-05-17 10:46:01 MarkDuplicates Tracking 27138 as yet unmatched pairs. 27138 records in RAM.
INFO 2016-05-17 10:46:07 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 5s. Last read position: chrM:15,142
INFO 2016-05-17 10:46:07 MarkDuplicates Tracking 12770 as yet unmatched pairs. 12770 records in RAM.
INFO 2016-05-17 10:46:12 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 5s. Last read position: chrM:15,254
INFO 2016-05-17 10:46:12 MarkDuplicates Tracking 23092 as yet unmatched pairs. 23092 records in RAM.
INFO 2016-05-17 10:46:18 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 5s. Last read position: chrM:15,380
INFO 2016-05-17 10:46:18 MarkDuplicates Tracking 25326 as yet unmatched pairs. 25326 records in RAM.
INFO 2016-05-17 10:46:24 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 5s. Last read position: chrM:15,495
INFO 2016-05-17 10:46:24 MarkDuplicates Tracking 24256 as yet unmatched pairs. 24256 records in RAM.
INFO 2016-05-17 10:46:30 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 5s. Last read position: chrM:15,610
INFO 2016-05-17 10:46:30 MarkDuplicates Tracking 25570 as yet unmatched pairs. 25570 records in RAM.
INFO 2016-05-17 10:46:50 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 20s. Last read position: chrM:15,719
INFO 2016-05-17 10:46:50 MarkDuplicates Tracking 24658 as yet unmatched pairs. 24658 records in RAM.
INFO 2016-05-17 10:46:57 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 6s. Last read position: chrM:15,818
INFO 2016-05-17 10:46:57 MarkDuplicates Tracking 39584 as yet unmatched pairs. 39584 records in RAM.
INFO 2016-05-17 10:47:02 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 5s. Last read position: chrM:16,012
INFO 2016-05-17 10:47:02 MarkDuplicates Tracking 24020 as yet unmatched pairs. 24020 records in RAM.
INFO 2016-05-17 10:47:08 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 5s. Last read position: chrM:16,290
INFO 2016-05-17 10:47:08 MarkDuplicates Tracking 17862 as yet unmatched pairs. 17862 records in RAM.
INFO 2016-05-17 10:47:14 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 5s. Last read position: chrM:16,396
INFO 2016-05-17 10:47:14 MarkDuplicates Tracking 31508 as yet unmatched pairs. 31508 records in RAM.
INFO 2016-05-17 10:47:19 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 5s. Last read position: chrM:16,528
INFO 2016-05-17 10:47:19 MarkDuplicates Tracking 7736 as yet unmatched pairs. 7736 records in RAM.
INFO 2016-05-17 10:47:24 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:16:13s. Time for last 1,000,000: 4s. Last read position: chrX:104,421,145
INFO 2016-05-17 10:47:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-05-17 10:47:27 MarkDuplicates Read 124559076 records. 0 pairs never matched.
INFO 2016-05-17 10:47:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 2417309280; totalMemory: 2445279232; maxMemory: 3817865216
INFO 2016-05-17 10:47:32 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk.
INFO 2016-05-17 10:47:32 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-05-17 10:49:24 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-05-17 10:50:26 MarkDuplicates Sorting list of duplicate records.
INFO 2016-05-17 10:50:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 2621386712; totalMemory: 3603431424; maxMemory: 3817865216
INFO 2016-05-17 10:50:33 MarkDuplicates Marking 89444602 records as duplicates.
INFO 2016-05-17 10:50:33 MarkDuplicates Found 41329182 optical duplicate clusters.
INFO 2016-05-17 10:53:14 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:39s. Time for last 10,000,000: 159s. Last read position: chr16:55,764,373
INFO 2016-05-17 10:56:01 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:05:27s. Time for last 10,000,000: 167s. Last read position: chr22:28,614,815
INFO 2016-05-17 10:58:39 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:08:04s. Time for last 10,000,000: 157s. Last read position: chr5:134,262,729
INFO 2016-05-17 11:00:55 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:10:21s. Time for last 10,000,000: 136s. Last read position: chrM:333
INFO 2016-05-17 11:02:53 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:12:18s. Time for last 10,000,000: 117s. Last read position: chrM:2,380
INFO 2016-05-17 11:04:48 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:14:14s. Time for last 10,000,000: 115s. Last read position: chrM:3,616
INFO 2016-05-17 11:06:37 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:16:02s. Time for last 10,000,000: 108s. Last read position: chrM:6,278
INFO 2016-05-17 11:07:55 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:17:21s. Time for last 10,000,000: 78s. Last read position: chrM:8,612
INFO 2016-05-17 11:09:09 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:18:35s. Time for last 10,000,000: 73s. Last read position: chrM:11,185
INFO 2016-05-17 11:10:22 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:19:47s. Time for last 10,000,000: 72s. Last read position: chrM:12,993
INFO 2016-05-17 11:11:38 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:21:03s. Time for last 10,000,000: 75s. Last read position: chrM:14,592
INFO 2016-05-17 11:12:54 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:22:20s. Time for last 10,000,000: 76s. Last read position: chrM:16,012
INFO 2016-05-17 11:13:35 MarkDuplicates Before output close freeMemory: 3639002312; totalMemory: 3669491712; maxMemory: 3817865216
INFO 2016-05-17 11:13:35 MarkDuplicates After output close freeMemory: 3639001256; totalMemory: 3669491712; maxMemory: 3817865216
[Tue May 17 11:13:35 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 42.43 minutes.
Runtime.totalMemory()=3669491712
[bam_sort_core] merging from 90 files...
|
| Num | 14 | | ID | task.postalign_bam.nmsrt_bam_rep1.line_321.id_19 | | Name | nmsrt_bam rep1 | | Thread | thread_20 | | PID | 53709 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:35:03 | | End | 2016-05-17 12:52:20 | | Elapsed | 00:17:16 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
| | Dependencies | | |
# SYS command. line 323
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 325
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.nmsrt
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 25 files...
|
| Num | 15 | | ID | task.postalign_bam.bam_to_bedpe_rep1.line_425.id_20 | | Name | bam_to_bedpe rep1 | | Thread | thread_20 | | PID | 54730 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:52:20 | | End | 2016-05-17 12:54:44 | | Elapsed | 00:02:24 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Dependencies | nmsrt_bam rep1
nmsrt_bam rep1
| |
# SYS command. line 427
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 430
bedtools bamtobed -bedpe -mate1 -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 16 | | ID | task.postalign_bed.subsample_bedpe_rep1.line_116.id_21 | | Name | subsample_bedpe rep1 | | Thread | thread_20 | | PID | 54830 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:54:46 | | End | 2016-05-17 12:56:27 | | Elapsed | 00:01:41 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
| | Dependencies | | |
# SYS command. line 118
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 120
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | grep -v "chrM" | shuf -n 17500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 17 | | ID | task.postalign_bam.bedpe_to_tag_rep1.line_465.id_22 | | Name | bedpe_to_tag rep1 | | Thread | thread_20 | | PID | 54911 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:56:28 | | End | 2016-05-17 12:58:09 | | Elapsed | 00:01:41 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
| | Dependencies | | |
# SYS command. line 467
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 469
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
# SYS command. line 472
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz; mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.rm_chr.tmp.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 18 | | ID | task.postalign_bed.shift_tag_rep1.line_140.id_23 | | Name | shift_tag rep1 | | Thread | thread_20 | | PID | 54980 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:58:10 | | End | 2016-05-17 12:59:19 | | Elapsed | 00:01:09 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Dependencies | | |
# SYS command. line 142
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 144
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 19 | | ID | task.postalign_bed.subsample_bedpe2tagrep1.line_89.id_24 | | Name | subsample_bedpe2tagrep1 | | Thread | thread_20 | | PID | 55045 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 12:59:20 | | End | 2016-05-17 13:00:16 | | Elapsed | 00:00:55 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
| | Dependencies | | |
# SYS command. line 91
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 95
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz | \
grep -v "chrM" | shuf -n 25000000 | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 20 | | ID | task.postalign_bed.xcor_rep1.line_165.id_25 | | Name | xcor rep1 | | Thread | thread_20 | | PID | 55124 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 13:00:17 | | End | 2016-05-17 13:23:14 | | Elapsed | 00:22:56 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
| | Dependencies | | |
# SYS command. line 167
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 171
Rscript $(which run_spp_nodups.R) -rf \
-c=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf -out=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc -speak=0
# SYS command. line 174
sed -r 's/,[^\t]+//g' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp
# SYS command. line 175
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc.tmp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 0
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.plot.pdf
result filename: /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlign.gz
opened /tmp/RtmpDfzM0T/ATAC15-trimmed-pair1.trim.PE2SE.nodup.25.tagAlignd7ef550c090
done. read 16445602 fragments
ChIP data read length 62
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.147887
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.270754928929814
Top 3 estimates for fragment length 0
Window half size 380
Phantom peak location 55
Phantom peak Correlation 0.2914263
Normalized Strand cross-correlation coefficient (NSC) 1.830823
Relative Strand Cross correlation Coefficient (RSC) 0.8559883
Phantom Peak Quality Tag 0
null device
1
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Loading required package: caTools
|
| Num | 21 | | ID | task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_192.id_26 | | Name | macs2_atac rep1.pval0.1 | | Thread | thread_20 | | PID | 55126 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 13:00:17 | | End | 2016-05-17 13:13:29 | | Elapsed | 00:13:12 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 13:00:22:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 13:00:22: #1 read tag files...
INFO @ Tue, 17 May 2016 13:00:22: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:00:23: 1000000
INFO @ Tue, 17 May 2016 13:00:25: 2000000
INFO @ Tue, 17 May 2016 13:00:27: 3000000
INFO @ Tue, 17 May 2016 13:00:29: 4000000
INFO @ Tue, 17 May 2016 13:00:31: 5000000
INFO @ Tue, 17 May 2016 13:00:33: 6000000
INFO @ Tue, 17 May 2016 13:00:35: 7000000
INFO @ Tue, 17 May 2016 13:00:37: 8000000
INFO @ Tue, 17 May 2016 13:00:39: 9000000
INFO @ Tue, 17 May 2016 13:00:41: 10000000
INFO @ Tue, 17 May 2016 13:00:43: 11000000
INFO @ Tue, 17 May 2016 13:00:44: 12000000
INFO @ Tue, 17 May 2016 13:00:46: 13000000
INFO @ Tue, 17 May 2016 13:00:48: 14000000
INFO @ Tue, 17 May 2016 13:00:50: 15000000
INFO @ Tue, 17 May 2016 13:00:52: 16000000
INFO @ Tue, 17 May 2016 13:00:53: 17000000
INFO @ Tue, 17 May 2016 13:00:55: 18000000
INFO @ Tue, 17 May 2016 13:00:57: 19000000
INFO @ Tue, 17 May 2016 13:00:59: 20000000
INFO @ Tue, 17 May 2016 13:01:01: 21000000
INFO @ Tue, 17 May 2016 13:01:03: 22000000
INFO @ Tue, 17 May 2016 13:01:05: 23000000
INFO @ Tue, 17 May 2016 13:01:06: 24000000
INFO @ Tue, 17 May 2016 13:01:08: 25000000
INFO @ Tue, 17 May 2016 13:01:10: 26000000
INFO @ Tue, 17 May 2016 13:01:11: 27000000
INFO @ Tue, 17 May 2016 13:01:13: 28000000
INFO @ Tue, 17 May 2016 13:01:15: 29000000
INFO @ Tue, 17 May 2016 13:01:17: 30000000
INFO @ Tue, 17 May 2016 13:01:19: 31000000
INFO @ Tue, 17 May 2016 13:01:21: 32000000
INFO @ Tue, 17 May 2016 13:01:25: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:01:25: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:01:25: #1 total tags in treatment: 32891204
INFO @ Tue, 17 May 2016 13:01:25: #1 finished!
INFO @ Tue, 17 May 2016 13:01:25: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:01:25: #2 Skipped...
INFO @ Tue, 17 May 2016 13:01:25: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:01:25: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:01:25: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:01:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000...
INFO @ Tue, 17 May 2016 13:01:25: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:02:31: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:04:19: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 13:04:22: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.broadPeak
INFO @ Tue, 17 May 2016 13:04:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.gappedPeak
INFO @ Tue, 17 May 2016 13:04:26: Done!
INFO @ Tue, 17 May 2016 13:04:36:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 13:04:36: #1 read tag files...
INFO @ Tue, 17 May 2016 13:04:36: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:04:38: 1000000
INFO @ Tue, 17 May 2016 13:04:40: 2000000
INFO @ Tue, 17 May 2016 13:04:42: 3000000
INFO @ Tue, 17 May 2016 13:04:43: 4000000
INFO @ Tue, 17 May 2016 13:04:45: 5000000
INFO @ Tue, 17 May 2016 13:04:46: 6000000
INFO @ Tue, 17 May 2016 13:04:48: 7000000
INFO @ Tue, 17 May 2016 13:04:50: 8000000
INFO @ Tue, 17 May 2016 13:04:51: 9000000
INFO @ Tue, 17 May 2016 13:04:53: 10000000
INFO @ Tue, 17 May 2016 13:04:55: 11000000
INFO @ Tue, 17 May 2016 13:04:56: 12000000
INFO @ Tue, 17 May 2016 13:04:58: 13000000
INFO @ Tue, 17 May 2016 13:05:00: 14000000
INFO @ Tue, 17 May 2016 13:05:01: 15000000
INFO @ Tue, 17 May 2016 13:05:03: 16000000
INFO @ Tue, 17 May 2016 13:05:04: 17000000
INFO @ Tue, 17 May 2016 13:05:06: 18000000
INFO @ Tue, 17 May 2016 13:05:07: 19000000
INFO @ Tue, 17 May 2016 13:05:09: 20000000
INFO @ Tue, 17 May 2016 13:05:11: 21000000
INFO @ Tue, 17 May 2016 13:05:12: 22000000
INFO @ Tue, 17 May 2016 13:05:14: 23000000
INFO @ Tue, 17 May 2016 13:05:15: 24000000
INFO @ Tue, 17 May 2016 13:05:17: 25000000
INFO @ Tue, 17 May 2016 13:05:19: 26000000
INFO @ Tue, 17 May 2016 13:05:20: 27000000
INFO @ Tue, 17 May 2016 13:05:22: 28000000
INFO @ Tue, 17 May 2016 13:05:23: 29000000
INFO @ Tue, 17 May 2016 13:05:25: 30000000
INFO @ Tue, 17 May 2016 13:05:26: 31000000
INFO @ Tue, 17 May 2016 13:05:28: 32000000
INFO @ Tue, 17 May 2016 13:05:32: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:05:32: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:05:32: #1 total tags in treatment: 32891204
INFO @ Tue, 17 May 2016 13:05:32: #1 finished!
INFO @ Tue, 17 May 2016 13:05:32: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:05:32: #2 Skipped...
INFO @ Tue, 17 May 2016 13:05:32: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:05:32: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:05:32: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:05:32: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 13:05:32: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ...
INFO @ Tue, 17 May 2016 13:05:32: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:06:38: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 13:06:38: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_treat_pileup.bdg
INFO @ Tue, 17 May 2016 13:06:38: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_control_lambda.bdg
INFO @ Tue, 17 May 2016 13:06:38: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 13:06:38: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:13:15: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 13:13:20: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_peaks.narrowPeak
INFO @ Tue, 17 May 2016 13:13:23: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1_summits.bed
INFO @ Tue, 17 May 2016 13:13:25: Done!
|
| Num | 22 | | ID | task.callpeak_macs2.macs2_atac_rep1.line_192.id_27 | | Name | macs2_atac rep1 | | Thread | thread_20 | | PID | 55129 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 13:00:17 | | End | 2016-05-17 13:36:50 | | Elapsed | 00:36:32 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 13:00:22:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 13:00:22: #1 read tag files...
INFO @ Tue, 17 May 2016 13:00:22: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:00:23: 1000000
INFO @ Tue, 17 May 2016 13:00:25: 2000000
INFO @ Tue, 17 May 2016 13:00:27: 3000000
INFO @ Tue, 17 May 2016 13:00:29: 4000000
INFO @ Tue, 17 May 2016 13:00:31: 5000000
INFO @ Tue, 17 May 2016 13:00:33: 6000000
INFO @ Tue, 17 May 2016 13:00:35: 7000000
INFO @ Tue, 17 May 2016 13:00:37: 8000000
INFO @ Tue, 17 May 2016 13:00:39: 9000000
INFO @ Tue, 17 May 2016 13:00:42: 10000000
INFO @ Tue, 17 May 2016 13:00:45: 11000000
INFO @ Tue, 17 May 2016 13:00:47: 12000000
INFO @ Tue, 17 May 2016 13:00:48: 13000000
INFO @ Tue, 17 May 2016 13:00:50: 14000000
INFO @ Tue, 17 May 2016 13:00:52: 15000000
INFO @ Tue, 17 May 2016 13:00:54: 16000000
INFO @ Tue, 17 May 2016 13:00:56: 17000000
INFO @ Tue, 17 May 2016 13:00:58: 18000000
INFO @ Tue, 17 May 2016 13:01:00: 19000000
INFO @ Tue, 17 May 2016 13:01:02: 20000000
INFO @ Tue, 17 May 2016 13:01:03: 21000000
INFO @ Tue, 17 May 2016 13:01:05: 22000000
INFO @ Tue, 17 May 2016 13:01:07: 23000000
INFO @ Tue, 17 May 2016 13:01:08: 24000000
INFO @ Tue, 17 May 2016 13:01:10: 25000000
INFO @ Tue, 17 May 2016 13:01:12: 26000000
INFO @ Tue, 17 May 2016 13:01:14: 27000000
INFO @ Tue, 17 May 2016 13:01:16: 28000000
INFO @ Tue, 17 May 2016 13:01:18: 29000000
INFO @ Tue, 17 May 2016 13:01:20: 30000000
INFO @ Tue, 17 May 2016 13:01:22: 31000000
INFO @ Tue, 17 May 2016 13:01:24: 32000000
INFO @ Tue, 17 May 2016 13:01:29: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:01:29: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:01:29: #1 total tags in treatment: 32891204
INFO @ Tue, 17 May 2016 13:01:29: #1 finished!
INFO @ Tue, 17 May 2016 13:01:29: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:01:29: #2 Skipped...
INFO @ Tue, 17 May 2016 13:01:29: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:01:29: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:01:29: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:01:29: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Tue, 17 May 2016 13:01:29: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:02:34: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:04:06: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls
INFO @ Tue, 17 May 2016 13:04:09: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.broadPeak
INFO @ Tue, 17 May 2016 13:04:11: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.gappedPeak
INFO @ Tue, 17 May 2016 13:04:13: Done!
INFO @ Tue, 17 May 2016 13:04:23:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 13:04:23: #1 read tag files...
INFO @ Tue, 17 May 2016 13:04:23: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:04:25: 1000000
INFO @ Tue, 17 May 2016 13:04:27: 2000000
INFO @ Tue, 17 May 2016 13:04:29: 3000000
INFO @ Tue, 17 May 2016 13:04:31: 4000000
INFO @ Tue, 17 May 2016 13:04:32: 5000000
INFO @ Tue, 17 May 2016 13:04:34: 6000000
INFO @ Tue, 17 May 2016 13:04:35: 7000000
INFO @ Tue, 17 May 2016 13:04:37: 8000000
INFO @ Tue, 17 May 2016 13:04:39: 9000000
INFO @ Tue, 17 May 2016 13:04:40: 10000000
INFO @ Tue, 17 May 2016 13:04:42: 11000000
INFO @ Tue, 17 May 2016 13:04:43: 12000000
INFO @ Tue, 17 May 2016 13:04:45: 13000000
INFO @ Tue, 17 May 2016 13:04:47: 14000000
INFO @ Tue, 17 May 2016 13:04:48: 15000000
INFO @ Tue, 17 May 2016 13:04:50: 16000000
INFO @ Tue, 17 May 2016 13:04:51: 17000000
INFO @ Tue, 17 May 2016 13:04:53: 18000000
INFO @ Tue, 17 May 2016 13:04:54: 19000000
INFO @ Tue, 17 May 2016 13:04:56: 20000000
INFO @ Tue, 17 May 2016 13:04:58: 21000000
INFO @ Tue, 17 May 2016 13:04:59: 22000000
INFO @ Tue, 17 May 2016 13:05:01: 23000000
INFO @ Tue, 17 May 2016 13:05:02: 24000000
INFO @ Tue, 17 May 2016 13:05:04: 25000000
INFO @ Tue, 17 May 2016 13:05:06: 26000000
INFO @ Tue, 17 May 2016 13:05:07: 27000000
INFO @ Tue, 17 May 2016 13:05:09: 28000000
INFO @ Tue, 17 May 2016 13:05:10: 29000000
INFO @ Tue, 17 May 2016 13:05:12: 30000000
INFO @ Tue, 17 May 2016 13:05:14: 31000000
INFO @ Tue, 17 May 2016 13:05:15: 32000000
INFO @ Tue, 17 May 2016 13:05:19: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:05:19: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:05:19: #1 total tags in treatment: 32891204
INFO @ Tue, 17 May 2016 13:05:19: #1 finished!
INFO @ Tue, 17 May 2016 13:05:19: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:05:19: #2 Skipped...
INFO @ Tue, 17 May 2016 13:05:19: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:05:19: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:05:19: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:05:19: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 13:05:19: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Tue, 17 May 2016 13:05:19: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:06:25: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 13:06:25: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_treat_pileup.bdg
INFO @ Tue, 17 May 2016 13:06:25: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_control_lambda.bdg
INFO @ Tue, 17 May 2016 13:06:25: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 13:06:25: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:11:16: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.xls
INFO @ Tue, 17 May 2016 13:11:20: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_peaks.narrowPeak
INFO @ Tue, 17 May 2016 13:11:22: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_summits.bed
INFO @ Tue, 17 May 2016 13:11:22: Done!
INFO @ Tue, 17 May 2016 13:11:26: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 13:12:23: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 13:12:51: Build scoreTrackII...
INFO @ Tue, 17 May 2016 13:13:13: Calculate scores comparing treatment and control by 'FE'...
INFO @ Tue, 17 May 2016 13:16:39: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 13:18:43: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_FE.bdg'!
INFO @ Tue, 17 May 2016 13:23:40: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 13:25:20: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 13:25:49: Build scoreTrackII...
INFO @ Tue, 17 May 2016 13:26:31: Values in your input bedGraph files will be multiplied by 32.891204 ...
INFO @ Tue, 17 May 2016 13:31:00: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Tue, 17 May 2016 13:31:27: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 13:33:05: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf_ppois.bdg'!
|
| Num | 23 | | ID | task.postalign_bed.pool_tag_reps.line_405.id_28 | | Name | pool_tag reps | | Thread | thread_Root | | PID | 57459 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 13:36:51 | | End | 2016-05-17 13:38:13 | | Elapsed | 00:01:22 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
| | Dependencies | | |
# SYS command. line 407
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 408
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 24 | | ID | task.callpeak_macs2.macs2_atac_pooled.pval0.1.line_192.id_29 | | Name | macs2_atac pooled.pval0.1 | | Thread | thread_Root | | PID | 57540 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 13:38:14 | | End | 2016-05-17 14:09:59 | | Elapsed | 00:31:45 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -g "hs" -p 0.1 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_summits.bed
# SYS command. line 217
if [[ false == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 13:38:16:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 13:38:16: #1 read tag files...
INFO @ Tue, 17 May 2016 13:38:16: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:38:18: 1000000
INFO @ Tue, 17 May 2016 13:38:20: 2000000
INFO @ Tue, 17 May 2016 13:38:21: 3000000
INFO @ Tue, 17 May 2016 13:38:23: 4000000
INFO @ Tue, 17 May 2016 13:38:25: 5000000
INFO @ Tue, 17 May 2016 13:38:26: 6000000
INFO @ Tue, 17 May 2016 13:38:28: 7000000
INFO @ Tue, 17 May 2016 13:38:29: 8000000
INFO @ Tue, 17 May 2016 13:38:31: 9000000
INFO @ Tue, 17 May 2016 13:38:33: 10000000
INFO @ Tue, 17 May 2016 13:38:34: 11000000
INFO @ Tue, 17 May 2016 13:38:36: 12000000
INFO @ Tue, 17 May 2016 13:38:38: 13000000
INFO @ Tue, 17 May 2016 13:38:39: 14000000
INFO @ Tue, 17 May 2016 13:38:42: 15000000
INFO @ Tue, 17 May 2016 13:38:45: 16000000
INFO @ Tue, 17 May 2016 13:38:49: 17000000
INFO @ Tue, 17 May 2016 13:38:52: 18000000
INFO @ Tue, 17 May 2016 13:38:55: 19000000
INFO @ Tue, 17 May 2016 13:38:58: 20000000
INFO @ Tue, 17 May 2016 13:39:02: 21000000
INFO @ Tue, 17 May 2016 13:39:05: 22000000
INFO @ Tue, 17 May 2016 13:39:09: 23000000
INFO @ Tue, 17 May 2016 13:39:13: 24000000
INFO @ Tue, 17 May 2016 13:39:16: 25000000
INFO @ Tue, 17 May 2016 13:39:19: 26000000
INFO @ Tue, 17 May 2016 13:39:23: 27000000
INFO @ Tue, 17 May 2016 13:39:26: 28000000
INFO @ Tue, 17 May 2016 13:39:30: 29000000
INFO @ Tue, 17 May 2016 13:39:33: 30000000
INFO @ Tue, 17 May 2016 13:39:37: 31000000
INFO @ Tue, 17 May 2016 13:39:40: 32000000
INFO @ Tue, 17 May 2016 13:39:44: 33000000
INFO @ Tue, 17 May 2016 13:39:48: 34000000
INFO @ Tue, 17 May 2016 13:39:51: 35000000
INFO @ Tue, 17 May 2016 13:39:55: 36000000
INFO @ Tue, 17 May 2016 13:39:58: 37000000
INFO @ Tue, 17 May 2016 13:40:01: 38000000
INFO @ Tue, 17 May 2016 13:40:05: 39000000
INFO @ Tue, 17 May 2016 13:40:08: 40000000
INFO @ Tue, 17 May 2016 13:40:11: 41000000
INFO @ Tue, 17 May 2016 13:40:14: 42000000
INFO @ Tue, 17 May 2016 13:40:18: 43000000
INFO @ Tue, 17 May 2016 13:40:22: 44000000
INFO @ Tue, 17 May 2016 13:40:25: 45000000
INFO @ Tue, 17 May 2016 13:40:29: 46000000
INFO @ Tue, 17 May 2016 13:40:33: 47000000
INFO @ Tue, 17 May 2016 13:40:36: 48000000
INFO @ Tue, 17 May 2016 13:40:40: 49000000
INFO @ Tue, 17 May 2016 13:40:43: 50000000
INFO @ Tue, 17 May 2016 13:40:46: 51000000
INFO @ Tue, 17 May 2016 13:40:50: 52000000
INFO @ Tue, 17 May 2016 13:40:53: 53000000
INFO @ Tue, 17 May 2016 13:40:57: 54000000
INFO @ Tue, 17 May 2016 13:41:01: 55000000
INFO @ Tue, 17 May 2016 13:41:04: 56000000
INFO @ Tue, 17 May 2016 13:41:08: 57000000
INFO @ Tue, 17 May 2016 13:41:13: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:41:13: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:41:13: #1 total tags in treatment: 57041514
INFO @ Tue, 17 May 2016 13:41:13: #1 finished!
INFO @ Tue, 17 May 2016 13:41:13: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:41:13: #2 Skipped...
INFO @ Tue, 17 May 2016 13:41:13: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:41:13: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:41:13: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:41:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000...
INFO @ Tue, 17 May 2016 13:41:13: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:44:51: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:50:09: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 13:50:16: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.broadPeak
INFO @ Tue, 17 May 2016 13:50:20: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.gappedPeak
INFO @ Tue, 17 May 2016 13:50:23: Done!
INFO @ Tue, 17 May 2016 13:50:41:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 13:50:41: #1 read tag files...
INFO @ Tue, 17 May 2016 13:50:41: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:50:45: 1000000
INFO @ Tue, 17 May 2016 13:50:48: 2000000
INFO @ Tue, 17 May 2016 13:50:52: 3000000
INFO @ Tue, 17 May 2016 13:50:55: 4000000
INFO @ Tue, 17 May 2016 13:50:59: 5000000
INFO @ Tue, 17 May 2016 13:51:02: 6000000
INFO @ Tue, 17 May 2016 13:51:06: 7000000
INFO @ Tue, 17 May 2016 13:51:09: 8000000
INFO @ Tue, 17 May 2016 13:51:13: 9000000
INFO @ Tue, 17 May 2016 13:51:16: 10000000
INFO @ Tue, 17 May 2016 13:51:20: 11000000
INFO @ Tue, 17 May 2016 13:51:23: 12000000
INFO @ Tue, 17 May 2016 13:51:26: 13000000
INFO @ Tue, 17 May 2016 13:51:30: 14000000
INFO @ Tue, 17 May 2016 13:51:33: 15000000
INFO @ Tue, 17 May 2016 13:51:37: 16000000
INFO @ Tue, 17 May 2016 13:51:40: 17000000
INFO @ Tue, 17 May 2016 13:51:44: 18000000
INFO @ Tue, 17 May 2016 13:51:47: 19000000
INFO @ Tue, 17 May 2016 13:51:51: 20000000
INFO @ Tue, 17 May 2016 13:51:54: 21000000
INFO @ Tue, 17 May 2016 13:51:58: 22000000
INFO @ Tue, 17 May 2016 13:52:01: 23000000
INFO @ Tue, 17 May 2016 13:52:05: 24000000
INFO @ Tue, 17 May 2016 13:52:09: 25000000
INFO @ Tue, 17 May 2016 13:52:12: 26000000
INFO @ Tue, 17 May 2016 13:52:16: 27000000
INFO @ Tue, 17 May 2016 13:52:19: 28000000
INFO @ Tue, 17 May 2016 13:52:22: 29000000
INFO @ Tue, 17 May 2016 13:52:26: 30000000
INFO @ Tue, 17 May 2016 13:52:29: 31000000
INFO @ Tue, 17 May 2016 13:52:32: 32000000
INFO @ Tue, 17 May 2016 13:52:35: 33000000
INFO @ Tue, 17 May 2016 13:52:38: 34000000
INFO @ Tue, 17 May 2016 13:52:41: 35000000
INFO @ Tue, 17 May 2016 13:52:45: 36000000
INFO @ Tue, 17 May 2016 13:52:48: 37000000
INFO @ Tue, 17 May 2016 13:52:51: 38000000
INFO @ Tue, 17 May 2016 13:52:55: 39000000
INFO @ Tue, 17 May 2016 13:52:58: 40000000
INFO @ Tue, 17 May 2016 13:53:01: 41000000
INFO @ Tue, 17 May 2016 13:53:05: 42000000
INFO @ Tue, 17 May 2016 13:53:08: 43000000
INFO @ Tue, 17 May 2016 13:53:12: 44000000
INFO @ Tue, 17 May 2016 13:53:16: 45000000
INFO @ Tue, 17 May 2016 13:53:20: 46000000
INFO @ Tue, 17 May 2016 13:53:23: 47000000
INFO @ Tue, 17 May 2016 13:53:27: 48000000
INFO @ Tue, 17 May 2016 13:53:30: 49000000
INFO @ Tue, 17 May 2016 13:53:34: 50000000
INFO @ Tue, 17 May 2016 13:53:38: 51000000
INFO @ Tue, 17 May 2016 13:53:41: 52000000
INFO @ Tue, 17 May 2016 13:53:45: 53000000
INFO @ Tue, 17 May 2016 13:53:48: 54000000
INFO @ Tue, 17 May 2016 13:53:51: 55000000
INFO @ Tue, 17 May 2016 13:53:55: 56000000
INFO @ Tue, 17 May 2016 13:53:58: 57000000
INFO @ Tue, 17 May 2016 13:54:04: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:54:04: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:54:04: #1 total tags in treatment: 57041514
INFO @ Tue, 17 May 2016 13:54:04: #1 finished!
INFO @ Tue, 17 May 2016 13:54:04: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:54:04: #2 Skipped...
INFO @ Tue, 17 May 2016 13:54:04: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:54:04: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:54:04: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:54:04: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 13:54:04: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ...
INFO @ Tue, 17 May 2016 13:54:04: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:57:38: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 13:57:38: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_treat_pileup.bdg
INFO @ Tue, 17 May 2016 13:57:38: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_control_lambda.bdg
INFO @ Tue, 17 May 2016 13:57:38: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 13:57:38: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 14:09:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.xls
INFO @ Tue, 17 May 2016 14:09:40: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_peaks.narrowPeak
INFO @ Tue, 17 May 2016 14:09:46: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1_summits.bed
INFO @ Tue, 17 May 2016 14:09:51: Done!
|
| Num | 25 | | ID | task.callpeak_macs2.macs2_atac_pooled.line_192.id_30 | | Name | macs2_atac pooled | | Thread | thread_Root | | PID | 57542 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 2 | | Mem | | | | Start | 2016-05-17 13:38:14 | | End | 2016-05-17 14:58:42 | | Elapsed | 01:20:27 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig
| | Dependencies | | |
# SYS command. line 194
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 195
LC_COLLATE=C
# SYS command. line 197
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 --broad --keep-dup all
# SYS command. line 202
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.broadPeak.gz
# SYS command. line 203
sort -k 14gr,14gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz
# SYS command. line 204
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.broadPeak
# SYS command. line 205
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.gappedPeak
# SYS command. line 207
macs2 callpeak \
-t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -g "hs" -p 0.01 \
--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# SYS command. line 212
sort -k 8gr,8gr "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz
# SYS command. line 213
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.narrowPeak
# SYS command. line 214
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_peaks.xls
# SYS command. line 215
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_summits.bed
# SYS command. line 217
if [[ true == "true" ]]; then \
\
macs2 bdgcmp -t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m FE;\
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_FE.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.srt.bedgraph; \
\
# sval counts the number of tags per million in the (compressed) BED file; \
sval=$(wc -l <(zcat -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
\
macs2 bdgcmp \
-t "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg -c "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg \
--o-prefix "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf" -m ppois -S "${sval}"; \
slopBed -i "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph; \
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_ppois.bdg; \
\
sort -k1,1 -k2,2n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
bedGraphToBigWig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig"; \
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bedgraph /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.srt.bedgraph; \
\
fi
# SYS command. line 243
rm -f "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_treat_pileup.bdg "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf"_control_lambda.bdg
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
INFO @ Tue, 17 May 2016 13:38:16:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
INFO @ Tue, 17 May 2016 13:38:16: #1 read tag files...
INFO @ Tue, 17 May 2016 13:38:16: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:38:18: 1000000
INFO @ Tue, 17 May 2016 13:38:20: 2000000
INFO @ Tue, 17 May 2016 13:38:22: 3000000
INFO @ Tue, 17 May 2016 13:38:23: 4000000
INFO @ Tue, 17 May 2016 13:38:25: 5000000
INFO @ Tue, 17 May 2016 13:38:26: 6000000
INFO @ Tue, 17 May 2016 13:38:28: 7000000
INFO @ Tue, 17 May 2016 13:38:30: 8000000
INFO @ Tue, 17 May 2016 13:38:31: 9000000
INFO @ Tue, 17 May 2016 13:38:33: 10000000
INFO @ Tue, 17 May 2016 13:38:34: 11000000
INFO @ Tue, 17 May 2016 13:38:36: 12000000
INFO @ Tue, 17 May 2016 13:38:38: 13000000
INFO @ Tue, 17 May 2016 13:38:39: 14000000
INFO @ Tue, 17 May 2016 13:38:42: 15000000
INFO @ Tue, 17 May 2016 13:38:45: 16000000
INFO @ Tue, 17 May 2016 13:38:48: 17000000
INFO @ Tue, 17 May 2016 13:38:51: 18000000
INFO @ Tue, 17 May 2016 13:38:55: 19000000
INFO @ Tue, 17 May 2016 13:38:58: 20000000
INFO @ Tue, 17 May 2016 13:39:02: 21000000
INFO @ Tue, 17 May 2016 13:39:05: 22000000
INFO @ Tue, 17 May 2016 13:39:09: 23000000
INFO @ Tue, 17 May 2016 13:39:12: 24000000
INFO @ Tue, 17 May 2016 13:39:16: 25000000
INFO @ Tue, 17 May 2016 13:39:19: 26000000
INFO @ Tue, 17 May 2016 13:39:22: 27000000
INFO @ Tue, 17 May 2016 13:39:26: 28000000
INFO @ Tue, 17 May 2016 13:39:30: 29000000
INFO @ Tue, 17 May 2016 13:39:33: 30000000
INFO @ Tue, 17 May 2016 13:39:36: 31000000
INFO @ Tue, 17 May 2016 13:39:40: 32000000
INFO @ Tue, 17 May 2016 13:39:43: 33000000
INFO @ Tue, 17 May 2016 13:39:47: 34000000
INFO @ Tue, 17 May 2016 13:39:50: 35000000
INFO @ Tue, 17 May 2016 13:39:54: 36000000
INFO @ Tue, 17 May 2016 13:39:57: 37000000
INFO @ Tue, 17 May 2016 13:40:01: 38000000
INFO @ Tue, 17 May 2016 13:40:04: 39000000
INFO @ Tue, 17 May 2016 13:40:08: 40000000
INFO @ Tue, 17 May 2016 13:40:11: 41000000
INFO @ Tue, 17 May 2016 13:40:15: 42000000
INFO @ Tue, 17 May 2016 13:40:18: 43000000
INFO @ Tue, 17 May 2016 13:40:21: 44000000
INFO @ Tue, 17 May 2016 13:40:24: 45000000
INFO @ Tue, 17 May 2016 13:40:28: 46000000
INFO @ Tue, 17 May 2016 13:40:31: 47000000
INFO @ Tue, 17 May 2016 13:40:35: 48000000
INFO @ Tue, 17 May 2016 13:40:38: 49000000
INFO @ Tue, 17 May 2016 13:40:42: 50000000
INFO @ Tue, 17 May 2016 13:40:45: 51000000
INFO @ Tue, 17 May 2016 13:40:49: 52000000
INFO @ Tue, 17 May 2016 13:40:52: 53000000
INFO @ Tue, 17 May 2016 13:40:56: 54000000
INFO @ Tue, 17 May 2016 13:40:59: 55000000
INFO @ Tue, 17 May 2016 13:41:03: 56000000
INFO @ Tue, 17 May 2016 13:41:06: 57000000
INFO @ Tue, 17 May 2016 13:41:12: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:41:12: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:41:12: #1 total tags in treatment: 57041514
INFO @ Tue, 17 May 2016 13:41:12: #1 finished!
INFO @ Tue, 17 May 2016 13:41:12: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:41:12: #2 Skipped...
INFO @ Tue, 17 May 2016 13:41:12: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:41:12: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:41:12: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:41:12: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000...
INFO @ Tue, 17 May 2016 13:41:12: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:44:49: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 13:49:30: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls
INFO @ Tue, 17 May 2016 13:49:36: #4 Write broad peak in broadPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.broadPeak
INFO @ Tue, 17 May 2016 13:49:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.gappedPeak
INFO @ Tue, 17 May 2016 13:49:43: Done!
INFO @ Tue, 17 May 2016 13:49:59:
# Command line: callpeak -t /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz -f BED -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
INFO @ Tue, 17 May 2016 13:49:59: #1 read tag files...
INFO @ Tue, 17 May 2016 13:49:59: #1 read treatment tags...
INFO @ Tue, 17 May 2016 13:50:02: 1000000
INFO @ Tue, 17 May 2016 13:50:05: 2000000
INFO @ Tue, 17 May 2016 13:50:09: 3000000
INFO @ Tue, 17 May 2016 13:50:13: 4000000
INFO @ Tue, 17 May 2016 13:50:16: 5000000
INFO @ Tue, 17 May 2016 13:50:20: 6000000
INFO @ Tue, 17 May 2016 13:50:23: 7000000
INFO @ Tue, 17 May 2016 13:50:26: 8000000
INFO @ Tue, 17 May 2016 13:50:30: 9000000
INFO @ Tue, 17 May 2016 13:50:33: 10000000
INFO @ Tue, 17 May 2016 13:50:37: 11000000
INFO @ Tue, 17 May 2016 13:50:40: 12000000
INFO @ Tue, 17 May 2016 13:50:44: 13000000
INFO @ Tue, 17 May 2016 13:50:47: 14000000
INFO @ Tue, 17 May 2016 13:50:51: 15000000
INFO @ Tue, 17 May 2016 13:50:54: 16000000
INFO @ Tue, 17 May 2016 13:50:58: 17000000
INFO @ Tue, 17 May 2016 13:51:01: 18000000
INFO @ Tue, 17 May 2016 13:51:05: 19000000
INFO @ Tue, 17 May 2016 13:51:09: 20000000
INFO @ Tue, 17 May 2016 13:51:12: 21000000
INFO @ Tue, 17 May 2016 13:51:15: 22000000
INFO @ Tue, 17 May 2016 13:51:19: 23000000
INFO @ Tue, 17 May 2016 13:51:22: 24000000
INFO @ Tue, 17 May 2016 13:51:26: 25000000
INFO @ Tue, 17 May 2016 13:51:29: 26000000
INFO @ Tue, 17 May 2016 13:51:33: 27000000
INFO @ Tue, 17 May 2016 13:51:36: 28000000
INFO @ Tue, 17 May 2016 13:51:39: 29000000
INFO @ Tue, 17 May 2016 13:51:43: 30000000
INFO @ Tue, 17 May 2016 13:51:46: 31000000
INFO @ Tue, 17 May 2016 13:51:50: 32000000
INFO @ Tue, 17 May 2016 13:51:53: 33000000
INFO @ Tue, 17 May 2016 13:51:56: 34000000
INFO @ Tue, 17 May 2016 13:52:00: 35000000
INFO @ Tue, 17 May 2016 13:52:03: 36000000
INFO @ Tue, 17 May 2016 13:52:06: 37000000
INFO @ Tue, 17 May 2016 13:52:10: 38000000
INFO @ Tue, 17 May 2016 13:52:13: 39000000
INFO @ Tue, 17 May 2016 13:52:16: 40000000
INFO @ Tue, 17 May 2016 13:52:20: 41000000
INFO @ Tue, 17 May 2016 13:52:23: 42000000
INFO @ Tue, 17 May 2016 13:52:26: 43000000
INFO @ Tue, 17 May 2016 13:52:29: 44000000
INFO @ Tue, 17 May 2016 13:52:32: 45000000
INFO @ Tue, 17 May 2016 13:52:35: 46000000
INFO @ Tue, 17 May 2016 13:52:39: 47000000
INFO @ Tue, 17 May 2016 13:52:42: 48000000
INFO @ Tue, 17 May 2016 13:52:45: 49000000
INFO @ Tue, 17 May 2016 13:52:49: 50000000
INFO @ Tue, 17 May 2016 13:52:52: 51000000
INFO @ Tue, 17 May 2016 13:52:55: 52000000
INFO @ Tue, 17 May 2016 13:52:59: 53000000
INFO @ Tue, 17 May 2016 13:53:02: 54000000
INFO @ Tue, 17 May 2016 13:53:06: 55000000
INFO @ Tue, 17 May 2016 13:53:09: 56000000
INFO @ Tue, 17 May 2016 13:53:13: 57000000
INFO @ Tue, 17 May 2016 13:53:18: #1 tag size is determined as 113 bps
INFO @ Tue, 17 May 2016 13:53:18: #1 tag size = 113
INFO @ Tue, 17 May 2016 13:53:18: #1 total tags in treatment: 57041514
INFO @ Tue, 17 May 2016 13:53:18: #1 finished!
INFO @ Tue, 17 May 2016 13:53:18: #2 Build Peak Model...
INFO @ Tue, 17 May 2016 13:53:18: #2 Skipped...
INFO @ Tue, 17 May 2016 13:53:18: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Tue, 17 May 2016 13:53:18: #2 Use 150 as fragment length
INFO @ Tue, 17 May 2016 13:53:18: #3 Call peaks...
INFO @ Tue, 17 May 2016 13:53:18: #3 Going to call summits inside each peak ...
INFO @ Tue, 17 May 2016 13:53:18: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Tue, 17 May 2016 13:53:18: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 17 May 2016 13:56:54: #3 In the peak calling step, the following will be performed simultaneously:
INFO @ Tue, 17 May 2016 13:56:54: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_treat_pileup.bdg
INFO @ Tue, 17 May 2016 13:56:54: #3 Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_control_lambda.bdg
INFO @ Tue, 17 May 2016 13:56:54: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Tue, 17 May 2016 13:56:54: #3 Call peaks for each chromosome...
INFO @ Tue, 17 May 2016 14:07:09: #4 Write output xls file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.xls
INFO @ Tue, 17 May 2016 14:07:12: #4 Write peak in narrowPeak format file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_peaks.narrowPeak
INFO @ Tue, 17 May 2016 14:07:15: #4 Write summits bed file... /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_summits.bed
INFO @ Tue, 17 May 2016 14:07:16: Done!
INFO @ Tue, 17 May 2016 14:07:21: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 14:09:14: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 14:10:39: Build scoreTrackII...
INFO @ Tue, 17 May 2016 14:12:07: Calculate scores comparing treatment and control by 'FE'...
INFO @ Tue, 17 May 2016 14:21:38: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 14:26:55: Finished 'FE'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_FE.bdg'!
INFO @ Tue, 17 May 2016 14:37:27: Read and build treatment bedGraph...
INFO @ Tue, 17 May 2016 14:41:02: Read and build control bedGraph...
INFO @ Tue, 17 May 2016 14:41:51: Build scoreTrackII...
INFO @ Tue, 17 May 2016 14:42:32: Values in your input bedGraph files will be multiplied by 57.041514 ...
INFO @ Tue, 17 May 2016 14:47:20: Calculate scores comparing treatment and control by 'ppois'...
INFO @ Tue, 17 May 2016 14:48:19: Write bedGraph of scores...
INFO @ Tue, 17 May 2016 14:50:58: Finished 'ppois'! Please check '/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf_ppois.bdg'!
|
| Num | 26 | | ID | task.callpeak_etc.filt_top_peaks_rep1.line_25.id_31 | | Name | filt_top_peaks rep1 | | Thread | thread_Root | | PID | 59185 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:42 | | End | 2016-05-17 14:58:49 | | Elapsed | 00:00:06 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 27 | | ID | task.callpeak_etc.filt_top_peaks_rep1.line_25.id_32 | | Name | filt_top_peaks rep1 | | Thread | thread_Root | | PID | 59187 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:42 | | End | 2016-05-17 14:58:51 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 28 | | ID | task.callpeak_etc.filt_top_peaks_rep2.line_25.id_33 | | Name | filt_top_peaks rep2 | | Thread | thread_Root | | PID | 59190 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:42 | | End | 2016-05-17 14:58:51 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 29 | | ID | task.callpeak_etc.filt_top_peaks_rep2.line_25.id_34 | | Name | filt_top_peaks rep2 | | Thread | thread_Root | | PID | 59202 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:42 | | End | 2016-05-17 14:58:50 | | Elapsed | 00:00:08 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 30 | | ID | task.callpeak_etc.filt_top_peaks_pooled.line_25.id_35 | | Name | filt_top_peaks pooled | | Thread | thread_Root | | PID | 59215 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:43 | | End | 2016-05-17 14:58:49 | | Elapsed | 00:00:06 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 31 | | ID | task.callpeak_etc.filt_top_peaks_pooled.line_25.id_36 | | Name | filt_top_peaks pooled | | Thread | thread_Root | | PID | 59235 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:43 | | End | 2016-05-17 14:58:48 | | Elapsed | 00:00:05 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
| | Dependencies | | |
# SYS command. line 27
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 30
zcat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 32 | | ID | task.idr.idr2_rep1_rep2.line_61.id_37 | | Name | idr2 rep1-rep2 | | Thread | thread_Root | | PID | 59544 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 14:58:52 | | End | 2016-05-17 15:04:38 | | Elapsed | 00:05:46 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.png
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| | Dependencies | | |
# SYS command. line 63
if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 65
idr --samples /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/pooled_rep/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
--output-file /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
--plot --use-best-multisummit-IDR
# SYS command. line 69
idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')
# SYS command. line 72
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz
# SYS command. line 75
awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt \
| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz
# SYS command. line 78
bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.narrowPeak.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz; bedtools intersect -v -a /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
# SYS command. line 80
gzip -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.83 0.69 0.91 0.36]
Number of reported peaks - 344868/344868 (100.0%)
Number of peaks passing IDR cutoff of 0.1 - 180196/344868 (52.3%)
|
| Num | 33 | | ID | task.base.line_414.id_40 | | Name | task.base.line_414.id_40 | | Thread | thread_Root | | PID | 60380 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:38 | | End | 2016-05-17 15:04:39 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
|
| Num | 34 | | ID | task.base.line_414.id_41 | | Name | task.base.line_414.id_41 | | Thread | thread_Root | | PID | 60387 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:38 | | End | 2016-05-17 15:04:39 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| | Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
|
| Num | 35 | | ID | task.base.line_414.id_42 | | Name | task.base.line_414.id_42 | | Thread | thread_Root | | PID | 60398 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:38 | | End | 2016-05-17 15:04:39 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| | Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
|
| Num | 36 | | ID | task.base.line_414.id_43 | | Name | task.base.line_414.id_43 | | Thread | thread_Root | | PID | 60411 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:39 | | End | 2016-05-17 15:04:39 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
| | Dependencies | | |
# SYS command. line 416
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.13-col.bed.gz /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.13-col.bed.gz
|
| Num | 37 | | ID | task.idr.idr_final_qc.line_196.id_44 | | Name | idr final qc | | Thread | thread_Root | | PID | 60429 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:39 | | End | 2016-05-17 15:04:40 | | Elapsed | 00:00:01 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/IDR_final.qc
| | Dependencies | | |
# SYS command. line 198
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 200
echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/IDR_final.qc
# SYS command. line 201
echo -e "180380\t""0\trep1-rep2\trep1-rep2\tInfinity\tNaN\t0" >> /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/IDR_final.qc
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
| Num | 38 | | ID | task.postalign_bam.srt_bam_rep2.line_345.id_45 | | Name | srt_bam rep2 | | Thread | thread_79 | | PID | 60434 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:39 | | End | 2016-05-17 15:39:17 | | Elapsed | 00:34:37 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bam
| | Dependencies | | |
# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 95 files...
|
| Num | 39 | | ID | task.postalign_bam.srt_bam_rep1.line_345.id_46 | | Name | srt_bam rep1 | | Thread | thread_78 | | PID | 60445 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:04:40 | | End | 2016-05-17 15:54:58 | | Elapsed | 00:50:17 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bam
| | Dependencies | | |
# SYS command. line 347
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 353
samtools sort /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt
# SYS command. line 354
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bam
# SYS command. line 356
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bai; \
fi
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 136 files...
|
| Num | 40 | | ID | task.atac.ataqc_rep2.line_815.id_47 | | Name | ataqc rep2 | | Thread | thread_79 | | PID | 62333 | | | OK | false | | Exit Code | 0 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:39:18 | | End | 2016-05-17 15:39:18 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC16/ATAC16-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC16/ATAC16-trimmed-pair2.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.align.log
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.PE2SE_qc.html
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.PE2SE_qc.txt
| | Dependencies | | |
# SYS command. line 817
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 821
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 823
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2
# SYS command. line 825
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2 \
--outprefix ATAC16-trimmed-pair1.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC16/ATAC16-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC16/ATAC16-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep2/ATAC16-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep2/ATAC16-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
\
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-17 15:42:49 ProcessExecutor Warning messages:
ERROR 2016-05-17 15:42:49 ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:42:49 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:42:49 ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:42:49 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:42:49 ProcessExecutor 3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:42:49 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:42:49 ProcessExecutor 4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:42:49 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:42:49 ProcessExecutor 5: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:42:49 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 94 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
|
| Num | 41 | | ID | task.atac.ataqc_rep1.line_815.id_48 | | Name | ataqc rep1 | | Thread | thread_78 | | PID | 63385 | | | OK | false | | Exit Code | 0 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 1 | | Mem | | | | Start | 2016-05-17 15:54:59 | | End | 2016-05-17 15:54:59 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC15/ATAC15-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC15/ATAC15-trimmed-pair2.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.align.log
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
| | Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.PE2SE_qc.html
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.PE2SE_qc.txt
| | Dependencies | | |
# SYS command. line 817
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 821
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 823
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1
# SYS command. line 825
/users/pangwei/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1 \
--outdir /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1 \
--outprefix ATAC15-trimmed-pair1.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC15/ATAC15-trimmed-pair1.fastq.gz --fastq2 /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC15/ATAC15-trimmed-pair2.fastq.gz \
--alignedbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/qc/rep1/ATAC15-trimmed-pair1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/align/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.tagAlign.gz \
--bigwig /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/signal/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/macs2/rep1/ATAC15-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz \
\
--idr_peaks /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC15+16/peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR 2016-05-17 15:59:13 ProcessExecutor Warning messages:
ERROR 2016-05-17 15:59:13 ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:59:13 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:59:13 ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:59:13 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
ERROR 2016-05-17 15:59:13 ProcessExecutor 3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH, :
ERROR 2016-05-17 15:59:13 ProcessExecutor zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 134 files...
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