BigDataScript report: atac.bds

Script file /users/pangwei/bds_atac/atac.bds
Program ID atac.bds.20160513_181510_584
Start time 2016-05-13 18:15:10
Run time 00:00:24.924
Tasks executed 2
Tasks failed 2
Tasks failed names 
dedup_bam_PE rep1
dedup_bam_PE rep2
Arguments* [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
System* local
Cpus* 1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
thread_21 thread_Root 
 atac.bds.20160513_181510_584_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_6
thread_20 thread_Root 
 atac.bds.20160513_181510_584_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_215.id_7

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.dedup_bam_PE_rep2.line_215.id_6
Name dedup_bam_PE rep2
Thread thread_21
PID 101288
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-05-13 18:15:11
End 2016-05-13 18:15:11
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam
Output files /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-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
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Fri May 13 18:15:13 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-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
[Fri May 13 18:15:13 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	2016-05-13 18:15:13	MarkDuplicates	Start of doWork freeMemory: 254890176; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-13 18:15:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-13 18:15:13	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-13 18:15:15	MarkDuplicates	Read 0 records. 0 pairs never matched.
INFO	2016-05-13 18:15:17	MarkDuplicates	After buildSortedReadEndLists freeMemory: 137147104; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-13 18:15:17	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-13 18:15:33	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-13 18:15:33	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-13 18:15:33	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-13 18:15:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 255016784; totalMemory: 1212153856; maxMemory: 3817865216
INFO	2016-05-13 18:15:34	MarkDuplicates	Marking 0 records as duplicates.
INFO	2016-05-13 18:15:34	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-05-13 18:15:34	MarkDuplicates	Before output close freeMemory: 1209070976; totalMemory: 1212153856; maxMemory: 3817865216
INFO	2016-05-13 18:15:34	MarkDuplicates	After output close freeMemory: 1209136112; totalMemory: 1212153856; maxMemory: 3817865216
[Fri May 13 18:15:34 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.36 minutes.
Runtime.totalMemory()=1212153856
awk: cmd. line:1: fatal: division by zero attempted
Num 2
ID task.postalign_bam.dedup_bam_PE_rep1.line_215.id_7
Name dedup_bam_PE rep1
Thread thread_20
PID 101290
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-05-13 18:15:11
End 2016-05-13 18:15:11
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam
Output files /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-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
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Fri May 13 18:15:13 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-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
[Fri May 13 18:15:13 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	2016-05-13 18:15:13	MarkDuplicates	Start of doWork freeMemory: 254889872; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-13 18:15:13	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-05-13 18:15:13	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-05-13 18:15:15	MarkDuplicates	Read 0 records. 0 pairs never matched.
INFO	2016-05-13 18:15:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 137146824; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-05-13 18:15:16	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-05-13 18:15:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-05-13 18:15:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-05-13 18:15:31	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-05-13 18:15:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 255016504; totalMemory: 1212153856; maxMemory: 3817865216
INFO	2016-05-13 18:15:32	MarkDuplicates	Marking 0 records as duplicates.
INFO	2016-05-13 18:15:32	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-05-13 18:15:32	MarkDuplicates	Before output close freeMemory: 1209070696; totalMemory: 1212153856; maxMemory: 3817865216
INFO	2016-05-13 18:15:32	MarkDuplicates	After output close freeMemory: 1209135832; totalMemory: 1212153856; maxMemory: 3817865216
[Fri May 13 18:15:32 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.33 minutes.
Runtime.totalMemory()=1212153856
awk: cmd. line:1: fatal: division by zero attempted

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
string _LMFILES_ /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/samtools/1.2:/software/modulefiles/bedtools/2.23.0:/software/modulefiles/rsem/1.2.21
string _ZSH_TMUX_FIXED_CONFIG /users/pangwei/.oh-my-zsh/plugins/tmux/tmux.extra.conf
bool allowEmpty false
string[] args [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19]
string C_INCLUDE_PATH /software/samtools/samtools-1.2/include/htslib
bool canFail false
int cpus 1
int cpusLocal 48
int day 86400
real E 2.718281828459045
int G 1073741824
string HOME /users/pangwei/
int hour 3600
int K 1024
string LANG en_US.UTF-8
string LC_CTYPE en_US.UTF-8
string LD_LIBRARY_PATH /software/samtools/samtools-1.2/lib:/usr/local/cudnn-3/lib64/:/usr/local/cudnn-3/lib64/
string LESS -R
string LOADEDMODULES modsappsdir/modsappsdir:samtools/1.2:bedtools/2.23.0:rsem/1.2.21
string LOGNAME pangwei
string LSCOLORS Gxfxcxdxbxegedabagacad
int M 1048576
string MAIL /var/mail/pangwei
string MANPATH /software/samtools/samtools-1.2/share/man:/usr/share/man
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string MODULESAPPSDIR /software
string MODULESHOME /software/env_module/3.2.10
string node
string OLDPWD /srv/scratch/pangwei/mesoderm/bulk-atac
int P 1125899906842624
string PAGER less
string PATH /software/RSEM/rsem-1.2.21/:/software/bedtools/2.23.0/bin:/software/samtools/samtools-1.2/bin:/users/pangwei/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
real PI 3.141592653589793
string ppwd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string programName atac.bds
string programPath /users/pangwei/bds_atac/atac.bds
string PWD /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata
string PYTHONPATH /home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:/home/jisraeli/src/caffe_atac/python/:/users/pangwei/stemcells:
string queue
int retry 0
string SAMTOOLS_HOME /software/samtools/samtools-1.2/bin
string SHELL /usr/bin/zsh
string SHLVL 2
string SSH_AUTH_SOCK /tmp/ssh-5gr8qSU2WF/agent.74700
string SSH_CLIENT 171.65.76.244 36245 22
string SSH_CONNECTION 171.65.76.244 49273 171.65.76.236 22
string SSH_TTY /dev/pts/0
string system local
int T 1099511627776
string TERM screen
string THEANO_FLAGS device=gpu6,floatX=float32,warn_float64=warn,optimizer_excluding=cudnn
int timeout -1
string TMUX /tmp/tmux-1077/default,106699,3
string TMUX_PANE %3
string USER pangwei
string UTIL_SCRIPTS_DIR /users/pangwei/av_scripts
int walltimeout 8640000
int week 604800
string WWW /srv/www/kundaje/pangwei
string XDG_RUNTIME_DIR /run/user/1077
string XDG_SESSION_ID 1907
string ZSH /users/pangwei//.oh-my-zsh
string ZSH_TMUX_TERM screen