Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20161101_222024_123
Start time	2016-11-01 22:20:24
Run time	09:14:16.998
Tasks executed	15
Tasks failed	1
Tasks failed names	xcor rep1
Arguments*	[-title, SRR836472, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None
thread_41	thread_Root	chipseq.bds.20161101_222024_123_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161101_222024_123_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_12 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_15 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_18 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
thread_42	thread_Root	chipseq.bds.20161101_222024_123_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20161101_222024_123_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_13 chipseq.bds.20161101_222024_123_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20161101_222024_123_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_16 chipseq.bds.20161101_222024_123_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_17 chipseq.bds.20161101_222024_123_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_19

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	2663

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2016-11-01 22:20:26
End	2016-11-02 01:15:24
Elapsed	02:54:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.sai
Dependencies

 
# SYS command. line 110

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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 3 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.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--------------------
19419 (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] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.02 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 9.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 7.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.90 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 5.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 10.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 14.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 14.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 7.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 13.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 8.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 6.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.99 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.06 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 7.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.77 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.29 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 4.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 13.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 15.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 15.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 6.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 7.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 13.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 8.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.27 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 39944766 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz
[main] Real time: 3224.553 sec; CPU: 9108.264 sec

Num	2
ID	task.align_bwa.bwa_aln_ctl1.line_108.id_11
Name	bwa_aln ctl1
Thread	thread_42
PID	2673

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-11-01 22:20:26
End	2016-11-02 02:00:08
Elapsed	03:39:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai
Dependencies

 
# SYS command. line 110

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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 2 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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--------------------
34235 (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] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 8.02 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz
[main] Real time: 3058.601 sec; CPU: 6007.744 sec

Num	3
ID	task.align_bwa.bwa_sam_rep1.line_140.id_12
Name	bwa_sam rep1
Thread	thread_41
PID	2761

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2016-11-02 01:15:25
End	2016-11-02 04:50:24
Elapsed	03:34:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.flagstat.qc
Dependencies

 
# SYS command. line 142

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam

# SYS command. line 149

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.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--------------------
28604 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.38 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.28 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.49 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.83 sec
[bwa_aln_core] refine gapped alignments... 1.95 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.03 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.49 sec
[bwa_aln_core] refine gapped alignments... 1.88 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.43 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.80 sec
[bwa_aln_core] refine gapped alignments... 1.20 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.59 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.43 sec
[bwa_aln_core] refine gapped alignments... 1.76 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.35 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.02 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.39 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 9.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 7.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 5.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.95 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.88 sec
[bwa_aln_core] refine gapped alignments... 2.07 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.55 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.26 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.86 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.59 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.65 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.35 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.68 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.25 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.27 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 10.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 14.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 14.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.18 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 4.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.07 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.09 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.74 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.47 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 7.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 13.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 8.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 6.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.65 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.70 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.07 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.75 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.19 sec
[bwa_aln_core] refine gapped alignments... 1.28 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.08 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.49 sec
[bwa_aln_core] refine gapped alignments... 1.29 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 7.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.46 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.19 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 4.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.40 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.77 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.88 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.43 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.35 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.72 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.56 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.97 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.72 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.97 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.46 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.36 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 13.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.15 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 15.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.45 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 15.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.54 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.77 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.92 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.28 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 6.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.97 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.84 sec
[bwa_aln_core] refine gapped alignments... 1.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.82 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.14 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.69 sec
[bwa_aln_core] refine gapped alignments... 1.93 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.17 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.58 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.47 sec
[bwa_aln_core] refine gapped alignments... 2.07 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.38 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.55 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.50 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.01 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.74 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 7.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 2.19 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.58 sec
[bwa_aln_core] refine gapped alignments... 1.20 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 13.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.78 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 12.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.66 sec
[bwa_aln_core] refine gapped alignments... 2.18 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.17 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 8.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.68 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.68 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.59 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.74 sec
[bwa_aln_core] refine gapped alignments... 2.08 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.48 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.71 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.80 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 39944766 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz
[main] Real time: 1921.902 sec; CPU: 1851.348 sec

Num	4
ID	task.align_bwa.bwa_sam_ctl1.line_140.id_13
Name	bwa_sam ctl1
Thread	thread_42
PID	2779

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-11-02 02:00:09
End	2016-11-02 04:44:46
Elapsed	02:44:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc
Dependencies

 
# SYS command. line 142

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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--------------------
31002 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.80 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.57 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.48 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.87 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.80 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.24 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.46 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.53 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.62 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.93 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.22 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.86 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.86 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.09 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.47 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.30 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.00 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.87 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.93 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.94 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.65 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.70 sec
[bwa_aln_core] refine gapped alignments... 6.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.35 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.96 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.28 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.53 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.33 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.44 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.71 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.91 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.53 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.47 sec
[bwa_aln_core] refine gapped alignments... 1.92 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.12 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.20 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.65 sec
[bwa_aln_core] refine gapped alignments... 3.71 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.02 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.05 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz
[main] Real time: 1667.105 sec; CPU: 1578.120 sec

Num	5
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	2894

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-11-02 04:44:48
End	2016-11-02 05:45:16
Elapsed	01:00:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam
Dependencies

 
# SYS command. line 97

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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--------------------
5286 (process ID) old priority 0, new priority 10

Num	6
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_15
Name	dedup_bam_1 rep1
Thread	thread_41
PID	2895

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2016-11-02 04:50:25
End	2016-11-02 06:26:00
Elapsed	01:35:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam
Dependencies

 
# SYS command. line 97

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${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 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.bam | \
			    	sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.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--------------------
2114 (process ID) old priority 0, new priority 10

Num	7
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_16
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	2940

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-11-02 05:45:18
End	2016-11-02 06:04:12
Elapsed	00:18:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc
Dependencies

 
# SYS command. line 349

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

# SYS command. line 353

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 354

 export MAX_JAVA_MEM="12G"

# SYS command. line 359

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 368

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 380

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

   
--------------------Stdout--------------------
48193 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 05:58:40 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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
[Wed Nov 02 05:58:40 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 05:58:40	MarkDuplicates	Start of doWork freeMemory: 254881776; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 05:58:40	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 05:58:40	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 05:58:46	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr1:169,651,309
INFO	2016-11-02 05:58:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:58:52	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    5s.  Last read position: chr2:120,600,340
INFO	2016-11-02 05:58:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:58:58	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    5s.  Last read position: chr3:96,659,413
INFO	2016-11-02 05:58:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:04	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    5s.  Last read position: chr4:108,195,091
INFO	2016-11-02 05:59:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:10	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    6s.  Last read position: chr5:103,594,339
INFO	2016-11-02 05:59:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:16	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    5s.  Last read position: chr6:98,592,333
INFO	2016-11-02 05:59:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:24	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    8s.  Last read position: chr7:114,109,505
INFO	2016-11-02 05:59:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:28	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr8:121,515,352
INFO	2016-11-02 05:59:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:35	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    6s.  Last read position: chr10:14,536,964
INFO	2016-11-02 05:59:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:44	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    8s.  Last read position: chr11:32,924,585
INFO	2016-11-02 05:59:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:49	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    5s.  Last read position: chr12:41,050,039
INFO	2016-11-02 05:59:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 05:59:58	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    8s.  Last read position: chr13:80,878,598
INFO	2016-11-02 05:59:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 06:00:03	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    4s.  Last read position: chr15:12,027,335
INFO	2016-11-02 06:00:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 06:00:07	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    4s.  Last read position: chr16:56,024,589
INFO	2016-11-02 06:00:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 06:00:22	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:   14s.  Last read position: chr18:10,030,498
INFO	2016-11-02 06:00:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 06:00:26	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    4s.  Last read position: chrX:36,565,109
INFO	2016-11-02 06:00:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 06:00:29	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 06:00:31	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1994475840; totalMemory: 2068316160; maxMemory: 3817865216
INFO	2016-11-02 06:00:31	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 06:00:31	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 06:00:31	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 06:00:39	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 06:00:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1394550752; totalMemory: 2364014592; maxMemory: 3817865216
INFO	2016-11-02 06:00:40	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 06:00:40	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 06:02:47	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:02:07s.  Time for last 10,000,000:  127s.  Last read position: chr11:32,924,585
INFO	2016-11-02 06:04:11	MarkDuplicates	Before output close freeMemory: 2063497936; totalMemory: 2080899072; maxMemory: 3817865216
INFO	2016-11-02 06:04:12	MarkDuplicates	After output close freeMemory: 2083419824; totalMemory: 2100822016; maxMemory: 3817865216
[Wed Nov 02 06:04:12 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.53 minutes.
Runtime.totalMemory()=2100822016

Num	8
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_17
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	3005

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	2
Mem

Start	2016-11-02 06:04:14
End	2016-11-02 06:56:38
Elapsed	00:52:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc
Dependencies

 
# SYS command. line 146

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

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam

# SYS command. line 153

 sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				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{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; 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/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc

# SYS command. line 169

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

   
--------------------Stdout--------------------
3605 (process ID) old priority 0, new priority 10

Num	9
ID	task.postalign_bam.markdup_bam_picard_rep1.line_347.id_18
Name	markdup_bam_picard rep1
Thread	thread_41
PID	3046

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-11-02 06:26:01
End	2016-11-02 07:10:44
Elapsed	00:44:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.dup.qc
Dependencies

 
# SYS command. line 349

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

# SYS command. line 353

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 354

 export MAX_JAVA_MEM="12G"

# SYS command. line 359

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 368

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 380

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

   
--------------------Stdout--------------------
5085 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 07:05:09 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.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
[Wed Nov 02 07:05:09 PDT 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 07:05:09	MarkDuplicates	Start of doWork freeMemory: 254882264; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 07:05:09	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 07:05:09	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 07:05:09	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836472.2503832'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2016-11-02 07:05:12	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:134,092,857
INFO	2016-11-02 07:05:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:15	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    3s.  Last read position: chr2:30,734,179
INFO	2016-11-02 07:05:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:20	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr2:128,638,462
INFO	2016-11-02 07:05:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:25	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr3:60,652,993
INFO	2016-11-02 07:05:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:29	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    3s.  Last read position: chr4:8,674,791
INFO	2016-11-02 07:05:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:33	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    4s.  Last read position: chr4:130,325,503
INFO	2016-11-02 07:05:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:37	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    3s.  Last read position: chr5:75,044,875
INFO	2016-11-02 07:05:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:41	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr6:18,722,251
INFO	2016-11-02 07:05:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:45	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    3s.  Last read position: chr6:127,281,105
INFO	2016-11-02 07:05:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:49	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    4s.  Last read position: chr7:97,455,535
INFO	2016-11-02 07:05:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:52	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    2s.  Last read position: chr8:64,731,251
INFO	2016-11-02 07:05:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:55	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    2s.  Last read position: chr9:39,709,055
INFO	2016-11-02 07:05:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:05:58	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    3s.  Last read position: chr9:124,034,023
INFO	2016-11-02 07:05:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:02	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    4s.  Last read position: chr10:99,577,468
INFO	2016-11-02 07:06:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:15	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:   13s.  Last read position: chr11:70,171,972
INFO	2016-11-02 07:06:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:18	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    2s.  Last read position: chr12:8,693,571
INFO	2016-11-02 07:06:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:22	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    4s.  Last read position: chr13:21,322,348
INFO	2016-11-02 07:06:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:26	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr14:19,975,125
INFO	2016-11-02 07:06:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:30	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    4s.  Last read position: chr15:32,097,665
INFO	2016-11-02 07:06:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:34	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    4s.  Last read position: chr16:23,364,412
INFO	2016-11-02 07:06:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:40	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    5s.  Last read position: chr17:32,222,341
INFO	2016-11-02 07:06:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:42	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    2s.  Last read position: chr18:51,945,843
INFO	2016-11-02 07:06:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:45	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chrX:7,679,834
INFO	2016-11-02 07:06:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:06:47	MarkDuplicates	Read 23520999 records. 0 pairs never matched.
INFO	2016-11-02 07:06:49	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1637982328; totalMemory: 1715470336; maxMemory: 3817865216
INFO	2016-11-02 07:06:49	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 07:06:50	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 07:06:50	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 07:06:56	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 07:06:57	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1980449496; totalMemory: 2954362880; maxMemory: 3817865216
INFO	2016-11-02 07:06:57	MarkDuplicates	Marking 10566424 records as duplicates.
INFO	2016-11-02 07:06:57	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 07:08:31	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:34s.  Time for last 10,000,000:   94s.  Last read position: chr7:97,455,535
INFO	2016-11-02 07:10:07	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:10s.  Time for last 10,000,000:   96s.  Last read position: chr16:23,364,412
INFO	2016-11-02 07:10:39	MarkDuplicates	Before output close freeMemory: 2840598120; totalMemory: 2863136768; maxMemory: 3817865216
INFO	2016-11-02 07:10:39	MarkDuplicates	After output close freeMemory: 2828014152; totalMemory: 2850553856; maxMemory: 3817865216
[Wed Nov 02 07:10:42 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.56 minutes.
Runtime.totalMemory()=2850553856

Num	10
ID	task.postalign_bam.bam_to_tag_ctl1.line_504.id_19
Name	bam_to_tag ctl1
Thread	thread_42
PID	3092

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2016-11-02 06:56:39
End	2016-11-02 07:18:25
Elapsed	00:21:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 506

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

# SYS command. line 509

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz

# SYS command. line 511

 echo

# SYS command. line 513

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

   
--------------------Stdout--------------------
6586 (process ID) old priority 0, new priority 10

Waiting for 48 seconds.

Num	11
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
Name	dedup_bam_2 rep1
Thread	thread_41
PID	3140

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	3
Mem

Start	2016-11-02 07:10:45
End	2016-11-02 07:20:41
Elapsed	00:09:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.pbc.qc
Dependencies

 
# SYS command. line 146

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

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam

# SYS command. line 153

 sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				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{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; 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/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.pbc.qc

# SYS command. line 169

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

   
--------------------Stdout--------------------
6191 (process ID) old priority 0, new priority 10

Num	12
ID	task.postalign_bam.bam_to_tag_rep1.line_504.id_21
Name	bam_to_tag rep1
Thread	thread_41
PID	3189

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2016-11-02 07:20:42
End	2016-11-02 07:31:10
Elapsed	00:10:27
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 506

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

# SYS command. line 509

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz

# SYS command. line 511

 echo

# SYS command. line 513

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

   
--------------------Stdout--------------------
9266 (process ID) old priority 0, new priority 10

Waiting for 27 seconds.

Num	13
ID	task.postalign_bed.subsample_tag_rep1.line_41.id_22
Name	subsample_tag rep1
Thread	thread_41
PID	3237

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2016-11-02 07:31:11
End	2016-11-02 07:33:55
Elapsed	00:02:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.15M.tagAlign.gz
Dependencies

 
# SYS command. line 43

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

# SYS command. line 46

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.15M.tagAlign.gz

# SYS command. line 49

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

   
--------------------Stdout--------------------
39565 (process ID) old priority 0, new priority 10
Waiting for 37 seconds.

Num	14
ID	task.postalign_bed.spr_rep1.line_247.id_23
Name	spr rep1
Thread	thread_41
PID	3239

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2016-11-02 07:31:12
End	2016-11-02 07:33:54
Elapsed	00:02:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr2/SRR836472.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 249

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

# SYS command. line 252

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz | wc -l )

# SYS command. line 253

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 257

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr2/SRR836472.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/pseudo_reps/rep1/pr1/SRR836472.nodup.01

# SYS command. line 265

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

   
--------------------Stdout--------------------
39567 (process ID) old priority 0, new priority 10
Waiting for 31 seconds.

Num	15
ID	task.postalign_bed.xcor_rep1.line_205.id_24
Name	xcor rep1
Thread	thread_41
PID	3277

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

Start	2016-11-02 07:33:57
End	2016-11-02 07:33:57
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.plot.pdf
Dependencies

 
# SYS command. line 207

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

# SYS command. line 210

 if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 216

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/align/rep1/SRR836472.nodup.15M.tagAlign.gz -p=3 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out/qc/rep1/SRR836472.nodup.15M.cc.qc

# SYS command. line 222

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

   
--------------------Stdout--------------------
9115 (process ID) old priority 0, new priority 10

  
--------------------Post mortem info--------------------
==============================================================
job_number:                 3277
exec_file:                  job_scripts/3277
submission_time:            Wed Nov  2 07:33:57 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/chipseq.bds.20161101_222024_123_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 51178 22,USER=imk1,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/18,LOGNAME=imk1,_=/usr/bin/bds,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect,PERL5LIB=/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5,DISPLAY=localhost:12.0,SGE_CELL=default,STY=35645.SRR836472.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_rUZelg,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 51178 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
parallel environment:  shm range: 3
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            queue instance "q@mitra" dropped because it is temporarily not available
                            queue instance "amd.q@mitra" dropped because it is temporarily not available
                            queue instance "q@wotan" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "amd.q@surya" dropped because it is full
                            queue instance "amd.q@kadru" dropped because it is full
                            queue instance "amd.q@kali" dropped because it is full
                            queue instance "amd.q@nandi" dropped because it is full
                            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@surya" dropped because it is full

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, SRR836472, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836472.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_rUZelg
string	LANG	en_US.UTF-8
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PATH	/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836472
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 51178 22
string	SSH_CONNECTION	171.65.77.8 51178 171.65.76.63 22
string	SSH_TTY	/dev/pts/18
string	STY	35645.SRR836472.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0