BigDataScript report: chipseq.bds

Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161113_130503_001
Start time	2016-11-13 13:05:03
Run time	00:01:03.864
Tasks executed	1
Tasks failed	0
Tasks failed names
Arguments*	[-title, SRR1370878_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370878_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
System*	sge
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_41	thread_Root	chipseq.bds.20161113_130503_001_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10
thread_42	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_sam_rep1.line_140.id_10
Name	bwa_sam rep1
Thread	thread_41
PID	8999

OK	false
Exit Code	0
Retries
State	RUNNING
Dep.	WAIT
Cpus	2
Mem

Start	2016-11-13 13:05:06
End	2016-11-13 13:05:06
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370878_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/align/rep1/SRR1370878_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/align/rep1/SRR1370878_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/qc/rep1/SRR1370878_1.flagstat.qc
Dependencies

 
# SYS command. line 142

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 147

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/align/rep1/SRR1370878_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370878_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/align/rep1/SRR1370878_1.bam

# SYS command. line 149

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/align/rep1/SRR1370878_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370878_1/out/qc/rep1/SRR1370878_1.flagstat.qc

# SYS command. line 151

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
17457 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate...

Global scope

Note: Global scope when program finished execution.

Type	Name	Value
int{}	filesize	{rep1=10438134084, ctl1=11033042636}
int{}	nth_rep	{rep1=2, ctl1=3}