Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_171019_723
Start time	2016-11-10 17:10:19
Run time	2 days 19:56:28.559
Tasks executed	2
Tasks failed	2
Tasks failed names	dedup_bam_1 ctl1 bwa_sam rep1
Arguments*	[-title, SRR1370893_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370893_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

Thread ID	Parent	Tasks
thread_Root	None
thread_42	thread_Root	chipseq.bds.20161110_171019_723_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
thread_41	thread_Root	chipseq.bds.20161110_171019_723_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_10
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	6903

OK	false
Exit Code	3
Retries
State	KILLED
Dep.	ERROR
Cpus	4
Mem

Start	2016-11-10 17:10:21
End	2016-11-10 17:15:26
Elapsed	00:05:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Dependencies

 
# SYS command. line 97

 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 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
			    fi

# SYS command. line 116

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

   
--------------------Stdout--------------------
11459 (process ID) old priority 0, new priority 10

Num	2
ID	task.align_bwa.bwa_sam_rep1.line_140.id_11
Name	bwa_sam rep1
Thread	thread_41
PID	6904

OK	false
Exit Code	3
Retries
State	RUNNING
Dep.	WAIT
Cpus	1
Mem

Start	2016-11-10 17:10:22
End	2016-11-10 17:10:22
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370893_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/rep1/SRR1370893_1.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/rep1/SRR1370893_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/qc/rep1/SRR1370893_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/SRR1370893_1/out/align/rep1/SRR1370893_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370893_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/rep1/SRR1370893_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/rep1/SRR1370893_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/qc/rep1/SRR1370893_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--------------------
11497 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.03 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.95 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.20 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 1.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.43 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.12 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.96 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.89 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.09 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.53 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.85 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.65 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.27 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.28 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.26 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.33 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.53 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 1.07 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.86 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.35 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.12 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.95 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.12 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.51 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.05 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.17 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.45 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.59 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.98 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.70 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 1.02 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.49 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.65 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.13 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.90 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.73 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.25 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.66 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.30 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.24 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.37 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.60 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.51 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.03 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.20 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.00 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.83 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 1.09 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 1.42 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.48 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 1.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.18 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.05 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.80 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.15 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.77 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 1.16 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.50 sec
[bwa_aln_core] refine gapped alignments... 3.10 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.85 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 1.20 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.10 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.27 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.89 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.26 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.79 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.64 sec
[bwa_aln_core] refine gapped alignments... 1.20 sec
[bwa_aln_core] print alignments... 1.19 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.74 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 1.11 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.08 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 1.08 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.42 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.10 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.25 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.09 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 1.25 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 1.32 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.83 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.56 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 1.24 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 1.17 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.22 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 1.14 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.09 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 1.18 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.51 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 19053937 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370893_1/out/align/rep1/SRR1370893_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370893_1.fastq.gz
[main] Real time: 1156.429 sec; CPU: 967.304 sec

Type	Name	Value
int{}	filesize	{rep1=2866489512, ctl1=11033042636}
int{}	nth_rep	{rep1=1, ctl1=4}

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope