BigDataScript report: atac.bds

Script file /users/pangwei/bds_atac/atac.bds
Program ID atac.bds.20160516_120116_681
Start time 2016-05-16 12:01:16
Run time 07:08:18.611
Tasks executed 5
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-out_dir, /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14, -num_rep, 2, -fastq1_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz, -fastq1_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz, -fastq2_1, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz, -fastq2_2, /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz, -subsample, 17500000, -true_rep, -species, hg19] 

		
  System*  local 

		
  Cpus*  1 

		
  Exit value  0 

	

	* Values in global scope when program finished execution.





	
 Timeline 

	
	
	






	
 Task Graph 

	






	
 Parallel (threads) details 

	

    
  Thread ID      Parent           	 Tasks  

	
  thread_Root   None 	 
  
 		 

	
  thread_20   thread_Root 	 
 atac.bds.20160516_120116_681_parallel_20/task.align_etc.trim_adapters_PE_rep1.line_57.id_6
atac.bds.20160516_120116_681_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_133.id_9
 
 		 

	
  thread_21   thread_Root 	 
 atac.bds.20160516_120116_681_parallel_21/task.align_etc.trim_adapters_PE_rep2.line_57.id_7
atac.bds.20160516_120116_681_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_133.id_8
atac.bds.20160516_120116_681_parallel_21/task.postalign_bam.dedup_bam_PE_rep2.line_215.id_10
 
 		 

	






	
 Task details 

	

    
  Task              Execution              Time   Dependencies       Task program, Errors, StdOut / StdErr  

    
  
 
  Num   1  
 
  ID   task.align_etc.trim_adapters_PE_rep2.line_57.id_7  
 
  Name   trim_adapters_PE rep2 
 
  Thread   thread_21  
 
  PID   109907  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:01:18  
 
  End   2016-05-16 13:14:13  
 
  Elapsed   01:12:55  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair2.trim.fastq.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

 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 61

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2

# SYS command. line 62

 $(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC14/ATAC14-trimmed-pair2.fastq.gz

# SYS command. line 63

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair2.trim.fastq
 
 
   
--------------------Stdout--------------------
ATAC14-trimmed-pair1.trim.fastq
ATAC14-trimmed-pair2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
45671279 sequences total
20535613 sequences trimmed with 0 mismatches
2983759 sequences trimmed with 1 mismatch
23 mean number of bases trimmed for reads requiring trimming

 
 		 

    
  
 
  Num   2  
 
  ID   task.align_etc.trim_adapters_PE_rep1.line_57.id_6  
 
  Name   trim_adapters_PE rep1 
 
  Thread   thread_20  
 
  PID   109916  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-05-16 12:01:18  
 
  End   2016-05-16 13:20:51  
 
  Elapsed   01:19:33  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 59

 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 61

 cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1

# SYS command. line 62

 $(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC13/ATAC13-trimmed-pair2.fastq.gz

# SYS command. line 63

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq
 
 
   
--------------------Stdout--------------------
ATAC13-trimmed-pair1.trim.fastq
ATAC13-trimmed-pair2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
48514285 sequences total
21219623 sequences trimmed with 0 mismatches
2842422 sequences trimmed with 1 mismatch
23 mean number of bases trimmed for reads requiring trimming

 
 		 

    
  
 
  Num   3  
 
  ID   task.align_bowtie2.bowtie2_PE_rep2.line_133.id_8  
 
  Name   bowtie2_PE rep2 
 
  Thread   thread_21  
 
  PID   111251  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 13:14:14  
 
  End   2016-05-16 19:06:39  
 
  Elapsed   05:52:24  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair2.trim.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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 38 files...

 
 		 

    
  
 
  Num   4  
 
  ID   task.align_bowtie2.bowtie2_PE_rep1.line_133.id_9  
 
  Name   bowtie2_PE rep1 
 
  Thread   thread_20  
 
  PID   111491  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2016-05-16 13:20:52  
 
  End   2016-05-16 13:20:52  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq.gz
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-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/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep1/ATAC13-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-trimmed-pair1.trim.PE2SE

# SYS command. line 142

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep1/ATAC13-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 40 files...

 
 		 

    
  
 
  Num   5  
 
  ID   task.postalign_bam.dedup_bam_PE_rep2.line_215.id_10  
 
  Name   dedup_bam_PE rep2 
 
  Thread   thread_21  
 
  PID   125731  
 
 		  
 
  OK   false   
 
  Exit Code   0   
 
  Retries    
 
  State   RUNNING  
 
  Dep.   WAIT  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2016-05-16 19:06:40  
 
  End   2016-05-16 19:06:40  
 
  Elapsed   00:00:00  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam
   
 
  Output files   /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt

# SYS command. line 239

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 269

 samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam

# SYS command. line 271

 if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
			cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bai; \
			fi

# SYS command. line 275

 samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 286

 samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam.tmp

# SYS command. line 287

 bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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/ATAC13+14/qc/rep2/ATAC14-trimmed-pair1.trim.PE2SE.nodup.pbc.qc

# SYS command. line 291

 rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 293

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-trimmed-pair1.trim.PE2SE.filt.bam

# SYS command. line 294

 rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC13+14/align/rep2/ATAC14-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

 
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value