Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161110_170955_180
Start time	2016-11-10 17:09:55
Run time	2 days 19:56:25.945
Tasks executed	2
Tasks failed	2
Tasks failed names	bwa_aln rep1 dedup_bam_1 ctl1
Arguments*	[-title, SRR1370881_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370881_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370881_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_170955_180_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11
thread_41	thread_Root	chipseq.bds.20161110_170955_180_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_bwa.bwa_aln_rep1.line_108.id_10
Name	bwa_aln rep1
Thread	thread_41
PID	6886

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

Start	2016-11-10 17:09:56
End	2016-11-10 17:15:01
Elapsed	00:05:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370881_1.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370881_1/out/align/rep1/SRR1370881_1.sai
Dependencies

 
# SYS command. line 110

 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 113

 bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370881_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370881_1/out/align/rep1/SRR1370881_1.sai

# SYS command. line 115

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

   
--------------------Stdout--------------------
10998 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.00 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.96 sec
[bwa_aln_core] write to the disk... 0.13 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.45 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.60 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.31 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.12 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.81 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.20 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.40 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.66 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.24 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.36 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.31 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.92 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 11.64 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 25194584 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370881_1.fastq.gz
[main] Real time: 9491.292 sec; CPU: 9435.604 sec

Num	2
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	6887

OK	false
Exit Code	3
Retries
State	RUNNING
Dep.	WAIT
Cpus	4
Mem

Start	2016-11-10 17:09:56
End	2016-11-10 17:09:56
Elapsed	00:00:00
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/SRR1370881_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/SRR1370881_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370881_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/SRR1370881_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370881_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/SRR1370881_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--------------------
14004 (process ID) old priority 0, new priority 10

Type	Name	Value
int{}	filesize	{rep1=3645272208, ctl1=11033042636}
int{}	nth_rep	{rep1=1, ctl1=4}

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope