Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20160928_164607_437
Start time	2016-09-28 16:46:07
Run time	12:12:25.183
Tasks executed	19
Tasks failed	0
Tasks failed names
Arguments*	[-title, WT, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20160928_164607_437/task.callpeak_spp.spp_rep1.line_54.id_25 chipseq.bds.20160928_164607_437/task.callpeak_idr.idr_final_qc.line_205.id_26 chipseq.bds.20160928_164607_437/task.graphviz.report.line_97.id_27 chipseq.bds.20160928_164607_437/task.report.pdf2png.line_324.id_32
thread_42	thread_Root	chipseq.bds.20160928_164607_437_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20160928_164607_437_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12 chipseq.bds.20160928_164607_437_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13 chipseq.bds.20160928_164607_437_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14 chipseq.bds.20160928_164607_437_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20160928_164607_437_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
thread_41	thread_Root	chipseq.bds.20160928_164607_437_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20160928_164607_437_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20160928_164607_437_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24

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	9615

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-09-28 16:46:09
End	2016-09-28 18:08:25
Elapsed	01:22:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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--------------------
11204 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.83 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.93 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.57 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.3% 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] 11796480 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.80 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.18 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.29 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.04 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.92 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.72 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.88 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.3% 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] 19660800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.74 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.67 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.44 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.3% 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] 24379392 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.32 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.04 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.46 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.66 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.10 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.10 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.4% 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] 34603008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.41 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.76 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.24 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.13 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.76 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.78 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.22 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.60 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.90 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.22 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.90 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.3% 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] 49807360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.71 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.04 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.55 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.3% 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] 56098816 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.05 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.39 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.23 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.26 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.05 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.96 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.3% 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] 65011712 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 66733966 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz
[main] Real time: 4930.281 sec; CPU: 14984.403 sec

Num	2
ID	task.align_bwa.bwa_aln_ctl1.line_108.id_11
Name	bwa_aln ctl1
Thread	thread_42
PID	9616

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

Start	2016-09-28 16:46:10
End	2016-09-28 17:16:26
Elapsed	00:30:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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--------------------
2542 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.88 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.86 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.90 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.53 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.19 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 22.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.67 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.29 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 5.46 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 23141323 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 1812.136 sec; CPU: 1806.876 sec

Num	3
ID	task.align_bwa.bwa_sam_ctl1.line_140.id_12
Name	bwa_sam ctl1
Thread	thread_42
PID	9639

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

Start	2016-09-28 17:16:28
End	2016-09-28 17:32:51
Elapsed	00:16:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.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/WT/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
30363 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.73 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.71 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.59 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.62 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.12 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.11 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.14 sec
[bwa_aln_core] 23141323 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/WT/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 574.479 sec; CPU: 474.072 sec

Num	4
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	9645

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

Start	2016-09-28 17:32:53
End	2016-09-28 17:37:31
Elapsed	00:04:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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--------------------
3728 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	5
ID	task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
Name	markdup_bam_picard ctl1
Thread	thread_42
PID	9653

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

Start	2016-09-28 17:37:33
End	2016-09-28 17:41:17
Elapsed	00:03:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.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/WT/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
10100 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Sep 28 17:37:43 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 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 Sep 28 17:37:43 PDT 2016] Executing as imk1@surya on Linux 4.2.0-27-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-28 17:37:43	MarkDuplicates	Start of doWork freeMemory: 255390144; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 17:37:43	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 17:37:43	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 17:37:54	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr1:174,151,470
INFO	2016-09-28 17:37:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:00	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    5s.  Last read position: chr2:135,780,411
INFO	2016-09-28 17:38:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:05	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    5s.  Last read position: chr3:122,530,375
INFO	2016-09-28 17:38:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:12	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    6s.  Last read position: chr4:135,044,888
INFO	2016-09-28 17:38:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:18	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    6s.  Last read position: chr5:135,067,778
INFO	2016-09-28 17:38:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:21	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr6:144,681,933
INFO	2016-09-28 17:38:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:23	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    2s.  Last read position: chr8:12,749,386
INFO	2016-09-28 17:38:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:27	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    3s.  Last read position: chr9:42,425,131
INFO	2016-09-28 17:38:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:30	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    2s.  Last read position: chr10:69,658,983
INFO	2016-09-28 17:38:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:34	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    4s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:38:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:39	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    4s.  Last read position: chr13:6,026,344
INFO	2016-09-28 17:38:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:41	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr14:54,434,282
INFO	2016-09-28 17:38:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:44	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    2s.  Last read position: chr15:98,839,731
INFO	2016-09-28 17:38:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:50	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    6s.  Last read position: chr17:62,456,013
INFO	2016-09-28 17:38:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:38:52	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    1s.  Last read position: chr19:38,585,732
INFO	2016-09-28 17:38:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:39:00	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 17:39:00	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2435841960; totalMemory: 2522349568; maxMemory: 3817799680
INFO	2016-09-28 17:39:00	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 17:39:00	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 17:39:00	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 17:39:05	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 17:39:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1920095968; totalMemory: 2896166912; maxMemory: 3817799680
INFO	2016-09-28 17:39:05	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 17:39:05	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 17:40:30	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:24s.  Time for last 10,000,000:   84s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:41:16	MarkDuplicates	Before output close freeMemory: 2865581904; totalMemory: 2893742080; maxMemory: 3817799680
INFO	2016-09-28 17:41:16	MarkDuplicates	After output close freeMemory: 2894547976; totalMemory: 2922708992; maxMemory: 3817799680
[Wed Sep 28 17:41:16 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.56 minutes.
Runtime.totalMemory()=2922708992

Num	6
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	9655

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

Start	2016-09-28 17:41:19
End	2016-09-28 17:45:52
Elapsed	00:04:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.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/WT/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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/WT/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
10656 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	7
ID	task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
Name	bam_to_tag ctl1
Thread	thread_42
PID	9658

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

Start	2016-09-28 17:45:53
End	2016-09-28 17:46:58
Elapsed	00:01:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.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--------------------
11251 (process ID) old priority 0, new priority 10

Waiting for 30 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	8
ID	task.align_bwa.bwa_sam_rep1.line_140.id_17
Name	bwa_sam rep1
Thread	thread_41
PID	9687

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-09-28 18:08:26
End	2016-09-28 21:36:57
Elapsed	03:28:30
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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--------------------
14508 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.88 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.30 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.11 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.30 sec
[bwa_aln_core] refine gapped alignments... 1.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.82 sec
[bwa_aln_core] refine gapped alignments... 1.82 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.95 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.44 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.16 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.48 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.66 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.73 sec
[bwa_aln_core] refine gapped alignments... 4.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.90 sec
[bwa_aln_core] refine gapped alignments... 3.85 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.86 sec
[bwa_aln_core] refine gapped alignments... 4.10 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.99 sec
[bwa_aln_core] refine gapped alignments... 4.55 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.56 sec
[bwa_aln_core] refine gapped alignments... 5.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.96 sec
[bwa_aln_core] refine gapped alignments... 5.50 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.08 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.77 sec
[bwa_aln_core] refine gapped alignments... 4.70 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.64 sec
[bwa_aln_core] refine gapped alignments... 5.62 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.35 sec
[bwa_aln_core] refine gapped alignments... 5.98 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.02 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.97 sec
[bwa_aln_core] refine gapped alignments... 5.93 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.40 sec
[bwa_aln_core] refine gapped alignments... 4.76 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.78 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.27 sec
[bwa_aln_core] refine gapped alignments... 5.94 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.77 sec
[bwa_aln_core] refine gapped alignments... 5.91 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.36 sec
[bwa_aln_core] refine gapped alignments... 5.88 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.91 sec
[bwa_aln_core] refine gapped alignments... 6.09 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.08 sec
[bwa_aln_core] refine gapped alignments... 5.30 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.90 sec
[bwa_aln_core] refine gapped alignments... 6.00 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.26 sec
[bwa_aln_core] refine gapped alignments... 5.91 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.73 sec
[bwa_aln_core] refine gapped alignments... 6.10 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.33 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.71 sec
[bwa_aln_core] refine gapped alignments... 5.87 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.84 sec
[bwa_aln_core] refine gapped alignments... 5.89 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.96 sec
[bwa_aln_core] refine gapped alignments... 4.72 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.15 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.28 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.66 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.03 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.63 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.27 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.11 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.63 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.91 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.92 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.72 sec
[bwa_aln_core] refine gapped alignments... 3.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.46 sec
[bwa_aln_core] refine gapped alignments... 3.48 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.62 sec
[bwa_aln_core] refine gapped alignments... 3.52 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.16 sec
[bwa_aln_core] refine gapped alignments... 3.55 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.49 sec
[bwa_aln_core] refine gapped alignments... 3.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.40 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.87 sec
[bwa_aln_core] refine gapped alignments... 3.82 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.78 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.36 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.68 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.46 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.97 sec
[bwa_aln_core] refine gapped alignments... 4.85 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.85 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.75 sec
[bwa_aln_core] refine gapped alignments... 5.02 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.88 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.02 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.50 sec
[bwa_aln_core] refine gapped alignments... 4.98 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.83 sec
[bwa_aln_core] refine gapped alignments... 4.88 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.96 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.41 sec
[bwa_aln_core] refine gapped alignments... 5.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.19 sec
[bwa_aln_core] refine gapped alignments... 5.30 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.85 sec
[bwa_aln_core] refine gapped alignments... 4.88 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.89 sec
[bwa_aln_core] refine gapped alignments... 4.99 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.95 sec
[bwa_aln_core] refine gapped alignments... 7.18 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.04 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.07 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.92 sec
[bwa_aln_core] refine gapped alignments... 5.70 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.49 sec
[bwa_aln_core] refine gapped alignments... 5.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.16 sec
[bwa_aln_core] refine gapped alignments... 5.60 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.44 sec
[bwa_aln_core] refine gapped alignments... 5.66 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.13 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.65 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.80 sec
[bwa_aln_core] refine gapped alignments... 16.77 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.37 sec
[bwa_aln_core] refine gapped alignments... 5.68 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.05 sec
[bwa_aln_core] refine gapped alignments... 5.62 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.76 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.72 sec
[bwa_aln_core] refine gapped alignments... 5.66 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.74 sec
[bwa_aln_core] refine gapped alignments... 5.93 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.86 sec
[bwa_aln_core] refine gapped alignments... 5.89 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.91 sec
[bwa_aln_core] refine gapped alignments... 5.85 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.99 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.69 sec
[bwa_aln_core] refine gapped alignments... 13.13 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 106.76 sec
[bwa_aln_core] refine gapped alignments... 17.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.63 sec
[bwa_aln_core] refine gapped alignments... 8.83 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.19 sec
[bwa_aln_core] refine gapped alignments... 8.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.16 sec
[bwa_aln_core] refine gapped alignments... 8.57 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.02 sec
[bwa_aln_core] refine gapped alignments... 8.54 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.68 sec
[bwa_aln_core] refine gapped alignments... 8.74 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.10 sec
[bwa_aln_core] refine gapped alignments... 7.95 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.37 sec
[bwa_aln_core] refine gapped alignments... 7.62 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.52 sec
[bwa_aln_core] refine gapped alignments... 7.53 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.95 sec
[bwa_aln_core] refine gapped alignments... 7.49 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.99 sec
[bwa_aln_core] refine gapped alignments... 7.78 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.42 sec
[bwa_aln_core] refine gapped alignments... 7.77 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.12 sec
[bwa_aln_core] refine gapped alignments... 7.58 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.23 sec
[bwa_aln_core] refine gapped alignments... 9.08 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.10 sec
[bwa_aln_core] refine gapped alignments... 8.02 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.83 sec
[bwa_aln_core] refine gapped alignments... 7.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.29 sec
[bwa_aln_core] refine gapped alignments... 7.73 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.74 sec
[bwa_aln_core] refine gapped alignments... 14.26 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.56 sec
[bwa_aln_core] refine gapped alignments... 20.19 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.13 sec
[bwa_aln_core] refine gapped alignments... 8.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.24 sec
[bwa_aln_core] refine gapped alignments... 9.77 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.15 sec
[bwa_aln_core] refine gapped alignments... 16.91 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.78 sec
[bwa_aln_core] refine gapped alignments... 9.68 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.58 sec
[bwa_aln_core] refine gapped alignments... 9.72 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.93 sec
[bwa_aln_core] refine gapped alignments... 9.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.70 sec
[bwa_aln_core] refine gapped alignments... 9.71 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.99 sec
[bwa_aln_core] refine gapped alignments... 9.50 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 98.23 sec
[bwa_aln_core] refine gapped alignments... 19.58 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 90.86 sec
[bwa_aln_core] refine gapped alignments... 9.14 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.77 sec
[bwa_aln_core] refine gapped alignments... 8.23 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.73 sec
[bwa_aln_core] refine gapped alignments... 8.08 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.75 sec
[bwa_aln_core] refine gapped alignments... 8.21 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.39 sec
[bwa_aln_core] refine gapped alignments... 8.24 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.63 sec
[bwa_aln_core] refine gapped alignments... 7.77 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.83 sec
[bwa_aln_core] refine gapped alignments... 8.64 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.07 sec
[bwa_aln_core] refine gapped alignments... 8.77 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.56 sec
[bwa_aln_core] refine gapped alignments... 7.59 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.14 sec
[bwa_aln_core] refine gapped alignments... 7.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.24 sec
[bwa_aln_core] refine gapped alignments... 7.69 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.14 sec
[bwa_aln_core] refine gapped alignments... 8.78 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.91 sec
[bwa_aln_core] refine gapped alignments... 7.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.20 sec
[bwa_aln_core] refine gapped alignments... 7.47 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.09 sec
[bwa_aln_core] refine gapped alignments... 7.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.21 sec
[bwa_aln_core] refine gapped alignments... 7.24 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.18 sec
[bwa_aln_core] refine gapped alignments... 7.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.31 sec
[bwa_aln_core] refine gapped alignments... 8.64 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.73 sec
[bwa_aln_core] refine gapped alignments... 8.08 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.02 sec
[bwa_aln_core] refine gapped alignments... 7.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.06 sec
[bwa_aln_core] refine gapped alignments... 10.82 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.88 sec
[bwa_aln_core] refine gapped alignments... 7.54 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.38 sec
[bwa_aln_core] refine gapped alignments... 9.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.25 sec
[bwa_aln_core] refine gapped alignments... 2.85 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.47 sec
[bwa_aln_core] refine gapped alignments... 8.86 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.81 sec
[bwa_aln_core] refine gapped alignments... 7.28 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.55 sec
[bwa_aln_core] refine gapped alignments... 7.99 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.37 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.51 sec
[bwa_aln_core] refine gapped alignments... 2.19 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.21 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.33 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.48 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.12 sec
[bwa_aln_core] refine gapped alignments... 1.82 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.55 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.31 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.24 sec
[bwa_aln_core] refine gapped alignments... 2.06 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.35 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.29 sec
[bwa_aln_core] refine gapped alignments... 1.96 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.77 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.56 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.21 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.60 sec
[bwa_aln_core] refine gapped alignments... 2.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.69 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.59 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.75 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.37 sec
[bwa_aln_core] refine gapped alignments... 2.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.60 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.35 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.61 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.88 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.83 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.31 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.82 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.19 sec
[bwa_aln_core] refine gapped alignments... 3.66 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.06 sec
[bwa_aln_core] refine gapped alignments... 3.80 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.32 sec
[bwa_aln_core] refine gapped alignments... 3.67 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.09 sec
[bwa_aln_core] refine gapped alignments... 6.82 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.65 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.50 sec
[bwa_aln_core] refine gapped alignments... 3.73 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.73 sec
[bwa_aln_core] refine gapped alignments... 3.86 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.98 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.36 sec
[bwa_aln_core] refine gapped alignments... 3.74 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.38 sec
[bwa_aln_core] refine gapped alignments... 3.92 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.29 sec
[bwa_aln_core] refine gapped alignments... 3.77 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.72 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.57 sec
[bwa_aln_core] refine gapped alignments... 3.98 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.45 sec
[bwa_aln_core] refine gapped alignments... 4.81 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.92 sec
[bwa_aln_core] refine gapped alignments... 4.70 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.85 sec
[bwa_aln_core] refine gapped alignments... 4.79 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.88 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.00 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.34 sec
[bwa_aln_core] refine gapped alignments... 4.27 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.53 sec
[bwa_aln_core] refine gapped alignments... 4.27 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.01 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.91 sec
[bwa_aln_core] refine gapped alignments... 5.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.95 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.55 sec
[bwa_aln_core] refine gapped alignments... 5.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.28 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.36 sec
[bwa_aln_core] refine gapped alignments... 5.75 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.63 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.75 sec
[bwa_aln_core] refine gapped alignments... 5.94 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.31 sec
[bwa_aln_core] refine gapped alignments... 6.23 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.74 sec
[bwa_aln_core] refine gapped alignments... 6.15 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.45 sec
[bwa_aln_core] refine gapped alignments... 5.90 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.52 sec
[bwa_aln_core] refine gapped alignments... 7.14 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.90 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.90 sec
[bwa_aln_core] refine gapped alignments... 8.96 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.85 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.01 sec
[bwa_aln_core] refine gapped alignments... 4.97 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.32 sec
[bwa_aln_core] refine gapped alignments... 6.17 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.78 sec
[bwa_aln_core] refine gapped alignments... 4.99 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.83 sec
[bwa_aln_core] refine gapped alignments... 8.04 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.35 sec
[bwa_aln_core] refine gapped alignments... 7.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.49 sec
[bwa_aln_core] refine gapped alignments... 6.15 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.69 sec
[bwa_aln_core] refine gapped alignments... 5.54 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.13 sec
[bwa_aln_core] refine gapped alignments... 1.92 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.18 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.51 sec
[bwa_aln_core] refine gapped alignments... 5.69 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.64 sec
[bwa_aln_core] refine gapped alignments... 6.61 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.35 sec
[bwa_aln_core] refine gapped alignments... 6.58 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.42 sec
[bwa_aln_core] refine gapped alignments... 6.68 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.41 sec
[bwa_aln_core] refine gapped alignments... 7.95 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.12 sec
[bwa_aln_core] refine gapped alignments... 5.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.36 sec
[bwa_aln_core] refine gapped alignments... 7.60 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.76 sec
[bwa_aln_core] refine gapped alignments... 7.31 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.77 sec
[bwa_aln_core] refine gapped alignments... 6.74 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.26 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.48 sec
[bwa_aln_core] refine gapped alignments... 7.30 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.10 sec
[bwa_aln_core] refine gapped alignments... 5.25 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.07 sec
[bwa_aln_core] refine gapped alignments... 7.63 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.06 sec
[bwa_aln_core] refine gapped alignments... 7.95 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.06 sec
[bwa_aln_core] refine gapped alignments... 8.16 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.20 sec
[bwa_aln_core] refine gapped alignments... 7.29 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.16 sec
[bwa_aln_core] refine gapped alignments... 6.68 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.09 sec
[bwa_aln_core] refine gapped alignments... 7.55 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.60 sec
[bwa_aln_core] refine gapped alignments... 6.82 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.80 sec
[bwa_aln_core] refine gapped alignments... 4.91 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.11 sec
[bwa_aln_core] refine gapped alignments... 7.54 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.32 sec
[bwa_aln_core] refine gapped alignments... 6.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.14 sec
[bwa_aln_core] refine gapped alignments... 6.72 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.05 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.55 sec
[bwa_aln_core] refine gapped alignments... 8.25 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.97 sec
[bwa_aln_core] refine gapped alignments... 5.91 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.32 sec
[bwa_aln_core] refine gapped alignments... 5.74 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.55 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.82 sec
[bwa_aln_core] refine gapped alignments... 7.16 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.42 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.32 sec
[bwa_aln_core] refine gapped alignments... 8.22 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.63 sec
[bwa_aln_core] refine gapped alignments... 8.27 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.79 sec
[bwa_aln_core] refine gapped alignments... 8.25 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.89 sec
[bwa_aln_core] refine gapped alignments... 8.27 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.72 sec
[bwa_aln_core] refine gapped alignments... 7.66 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.86 sec
[bwa_aln_core] refine gapped alignments... 7.90 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.88 sec
[bwa_aln_core] refine gapped alignments... 7.69 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.47 sec
[bwa_aln_core] refine gapped alignments... 8.24 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.85 sec
[bwa_aln_core] refine gapped alignments... 8.20 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 66733966 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/WT/out/align/rep1/wt_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz
[main] Real time: 12336.213 sec; CPU: 12239.344 sec

Num	9
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
Name	dedup_bam_1 rep1
Thread	thread_41
PID	9724

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-09-28 21:36:58
End	2016-09-28 21:41:58
Elapsed	00:04:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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--------------------
44963 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	10
ID	task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
Name	markdup_bam_picard rep1
Thread	thread_41
PID	9725

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

Start	2016-09-28 21:41:59
End	2016-09-28 21:49:37
Elapsed	00:07:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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--------------------
7648 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Sep 28 21:46:21 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 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 Sep 28 21:46:21 PDT 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-28 21:46:21	MarkDuplicates	Start of doWork freeMemory: 255390336; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 21:46:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 21:46:21	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-28 21:46:22	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836489.18372202'.  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	2016-09-28 21:46:27	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr1:74,248,297
INFO	2016-09-28 21:46:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:31	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    3s.  Last read position: chr1:133,308,363
INFO	2016-09-28 21:46:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:34	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    3s.  Last read position: chr1:179,593,079
INFO	2016-09-28 21:46:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:38	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    3s.  Last read position: chr2:28,464,099
INFO	2016-09-28 21:46:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:40	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    2s.  Last read position: chr2:73,442,188
INFO	2016-09-28 21:46:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:43	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr2:127,462,406
INFO	2016-09-28 21:46:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:45	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    1s.  Last read position: chr2:165,373,635
INFO	2016-09-28 21:46:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:48	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    3s.  Last read position: chr3:44,017,834
INFO	2016-09-28 21:46:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:50	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    1s.  Last read position: chr3:96,328,721
INFO	2016-09-28 21:46:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:51	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    1s.  Last read position: chr3:149,539,357
INFO	2016-09-28 21:46:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:55	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    3s.  Last read position: chr4:58,999,909
INFO	2016-09-28 21:46:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:57	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr4:123,254,736
INFO	2016-09-28 21:46:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:46:59	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr4:142,083,732
INFO	2016-09-28 21:46:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:04	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    4s.  Last read position: chr5:33,894,836
INFO	2016-09-28 21:47:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:05	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    1s.  Last read position: chr5:100,917,563
INFO	2016-09-28 21:47:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:12	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    6s.  Last read position: chr5:130,007,491
INFO	2016-09-28 21:47:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:14	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    1s.  Last read position: chr6:22,695,051
INFO	2016-09-28 21:47:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:16	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr6:83,114,794
INFO	2016-09-28 21:47:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:18	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    1s.  Last read position: chr6:124,663,273
INFO	2016-09-28 21:47:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:20	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    2s.  Last read position: chr7:25,105,976
INFO	2016-09-28 21:47:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:22	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    1s.  Last read position: chr7:72,240,107
INFO	2016-09-28 21:47:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:23	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    1s.  Last read position: chr7:116,093,093
INFO	2016-09-28 21:47:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:25	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    1s.  Last read position: chr8:9,976,101
INFO	2016-09-28 21:47:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:28	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:    2s.  Last read position: chr8:71,513,533
INFO	2016-09-28 21:47:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:29	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    1s.  Last read position: chr8:113,717,414
INFO	2016-09-28 21:47:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:31	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    1s.  Last read position: chr9:32,388,307
INFO	2016-09-28 21:47:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:32	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    1s.  Last read position: chr9:65,434,197
INFO	2016-09-28 21:47:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:34	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    1s.  Last read position: chr9:110,158,830
INFO	2016-09-28 21:47:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:38	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr10:39,811,715
INFO	2016-09-28 21:47:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:39	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    1s.  Last read position: chr10:80,420,355
INFO	2016-09-28 21:47:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:46	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    6s.  Last read position: chr10:127,381,117
INFO	2016-09-28 21:47:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:47	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    1s.  Last read position: chr11:49,956,038
INFO	2016-09-28 21:47:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:49	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    2s.  Last read position: chr11:76,314,872
INFO	2016-09-28 21:47:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:52	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    2s.  Last read position: chr11:100,577,049
INFO	2016-09-28 21:47:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:54	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    2s.  Last read position: chr11:120,690,466
INFO	2016-09-28 21:47:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:57	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    2s.  Last read position: chr12:76,016,783
INFO	2016-09-28 21:47:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:47:58	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    1s.  Last read position: chr12:113,104,117
INFO	2016-09-28 21:47:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:00	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    1s.  Last read position: chr13:51,413,583
INFO	2016-09-28 21:48:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:01	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    1s.  Last read position: chr13:108,459,784
INFO	2016-09-28 21:48:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:03	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    1s.  Last read position: chr14:54,494,391
INFO	2016-09-28 21:48:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:07	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    3s.  Last read position: chr14:118,768,241
INFO	2016-09-28 21:48:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:08	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    1s.  Last read position: chr15:71,508,000
INFO	2016-09-28 21:48:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:11	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    2s.  Last read position: chr15:97,794,536
INFO	2016-09-28 21:48:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:13	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    2s.  Last read position: chr16:29,247,114
INFO	2016-09-28 21:48:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:15	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    2s.  Last read position: chr16:93,890,591
INFO	2016-09-28 21:48:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:22	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    6s.  Last read position: chr17:32,270,081
INFO	2016-09-28 21:48:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:24	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    1s.  Last read position: chr17:71,196,158
INFO	2016-09-28 21:48:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:26	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    2s.  Last read position: chr18:36,740,030
INFO	2016-09-28 21:48:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:29	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    2s.  Last read position: chr18:87,487,067
INFO	2016-09-28 21:48:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:30	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    1s.  Last read position: chr19:41,263,283
INFO	2016-09-28 21:48:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:32	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    1s.  Last read position: chrX:75,764,230
INFO	2016-09-28 21:48:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 21:48:33	MarkDuplicates	Read 51543114 records. 0 pairs never matched.
INFO	2016-09-28 21:48:35	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1905309248; totalMemory: 1992425472; maxMemory: 3817799680
INFO	2016-09-28 21:48:35	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 21:48:35	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 21:48:35	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 21:48:46	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 21:48:48	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2029760720; totalMemory: 3008823296; maxMemory: 3817799680
INFO	2016-09-28 21:48:48	MarkDuplicates	Marking 34767689 records as duplicates.
INFO	2016-09-28 21:48:48	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 21:49:46	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:00:57s.  Time for last 10,000,000:   57s.  Last read position: chr3:149,539,357
INFO	2016-09-28 21:50:42	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:01:53s.  Time for last 10,000,000:   56s.  Last read position: chr7:25,105,976
INFO	2016-09-28 21:51:41	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:02:52s.  Time for last 10,000,000:   58s.  Last read position: chr10:80,420,355
INFO	2016-09-28 21:52:38	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:03:49s.  Time for last 10,000,000:   57s.  Last read position: chr14:54,494,391
INFO	2016-09-28 21:53:35	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:04:46s.  Time for last 10,000,000:   57s.  Last read position: chr19:41,263,283
INFO	2016-09-28 21:53:45	MarkDuplicates	Before output close freeMemory: 3073573944; totalMemory: 3103260672; maxMemory: 3817799680
INFO	2016-09-28 21:53:45	MarkDuplicates	After output close freeMemory: 3073438096; totalMemory: 3103129600; maxMemory: 3817799680
[Wed Sep 28 21:53:45 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 7.41 minutes.
Runtime.totalMemory()=3103129600

Num	11
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
Name	dedup_bam_2 rep1
Thread	thread_41
PID	9726

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-09-28 21:49:39
End	2016-09-28 21:58:50
Elapsed	00:09:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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/WT/out/qc/rep1/wt_allReps.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--------------------
40810 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	12
ID	task.postalign_bam.bam_to_tag_rep1.line_504.id_21
Name	bam_to_tag rep1
Thread	thread_41
PID	9727

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

Start	2016-09-28 21:58:52
End	2016-09-28 21:59:58
Elapsed	00:01:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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--------------------
31099 (process ID) old priority 0, new priority 10

Waiting for 28 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	13
ID	task.postalign_bed.subsample_tag_rep1.line_41.id_22
Name	subsample_tag rep1
Thread	thread_41
PID	9728

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

Start	2016-09-28 22:00:00
End	2016-09-28 22:01:14
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.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--------------------
31264 (process ID) old priority 0, new priority 10
Waiting for 26 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	14
ID	task.postalign_bed.spr_rep1.line_247.id_23
Name	spr rep1
Thread	thread_41
PID	9729

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

Start	2016-09-28 22:00:01
End	2016-09-28 22:01:13
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr2/wt_allReps.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/WT/out/align/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.nodup.

# SYS command. line 260

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

# SYS command. line 261

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

# SYS command. line 262

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

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/pseudo_reps/rep1/pr1/wt_allReps.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--------------------
31263 (process ID) old priority 0, new priority 10
Waiting for 21 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	15
ID	task.postalign_bed.xcor_rep1.line_205.id_24
Name	xcor rep1
Thread	thread_41
PID	9730

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	4
Mem

Start	2016-09-28 22:01:15
End	2016-09-28 22:12:46
Elapsed	00:11:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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/WT/out/align/rep1/wt_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.qc 

# SYS command. line 219

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

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.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--------------------
46307 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 4 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9730.1.q/RtmpO06Whi/wt_allReps.nodup.15M.tagAlignb525387c9c23
done. read 15000000 fragments
ChIP data read length 36 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1527084 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.470155881467305 
Top 3 estimates for fragment length 110 
Window half size 230 
Phantom peak location 40 
Phantom peak Correlation 0.3475234 
Normalized Strand cross-correlation coefficient (NSC) 3.078783 
Relative Strand Cross correlation Coefficient (RSC) 1.629481 
Phantom Peak Quality Tag 2 
null device 
          1 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools

Num	16
ID	task.callpeak_spp.spp_rep1.line_54.id_25
Name	spp rep1
Thread	thread_Root
PID	9731

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

Start	2016-09-28 22:12:48
End	2016-09-29 04:57:15
Elapsed	06:44:26
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf
Dependencies

 
# SYS command. line 56

 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 59

 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 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1 -speak=110 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

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

   
--------------------Stdout--------------------
32202 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 110 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/peak/spp/rep1/wt_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/rep1/wt_allReps.nodup.tagAlign.gz 
opened /tmp/9731.1.q/RtmpHFOFSv/wt_allReps.nodup.tagAlign7e0c63d50898
done. read 16775425 fragments
ChIP data read length 36 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9731.1.q/RtmpHFOFSv/mousePrimaryBCellInput.nodup.tagAlign7e0c6df32f89
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.1622832 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.499410085054225 
Top 3 estimates for fragment length 110 
Window half size 230 
Phantom peak location 40 
Phantom peak Correlation 0.3691204 
Normalized Strand cross-correlation coefficient (NSC) 3.077399 
Relative Strand Cross correlation Coefficient (RSC) 1.629914 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 1.684878  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.5935149  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000003 
Detected 430097 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 26 warnings (use warnings() to see them)

Num	17
ID	task.callpeak_idr.idr_final_qc.line_205.id_26
Name	idr final qc
Thread	thread_Root
PID	9777

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

Start	2016-09-29 04:57:16
End	2016-09-29 04:58:28
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/WT_IDR_final.qc
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 209

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/WT_IDR_final.qc

# SYS command. line 210

 echo -e "0\t""0\tN/A\tN/A\tNaN\tNaN\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/WT_IDR_final.qc

# SYS command. line 212

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

   
--------------------Stdout--------------------
6126 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	18
ID	task.graphviz.report.line_97.id_27
Name	report
Thread	thread_Root
PID	1128

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

Start	2016-09-29 04:58:29
End	2016-09-29 04:58:32
Elapsed	00:00:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 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 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/report/WT_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
1133 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Num	19
ID	task.report.pdf2png.line_324.id_32
Name	pdf2png
Thread	thread_Root
PID	1181

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

Start	2016-09-29 04:58:30
End	2016-09-29 04:58:32
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.pdf
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.png
Dependencies

 
# SYS command. line 325

 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 326

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT/out/qc/rep1/wt_allReps.nodup.15M.cc.plot.pdf

   
--------------------Stdout--------------------
1186 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, WT, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/WT/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $]
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DISPLAY	localhost:19.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
int	K	1024
string	KERAS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/keras
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_eHVWt0
string	LANG	en_US.UTF-8
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/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:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/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/WT
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/WT
string	PYTHONPATH	/software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SGE_CELL	default
string	SGE_ROOT	/var/lib/gridengine
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 58475 22
string	SSH_CONNECTION	171.65.77.8 58475 171.65.76.63 22
string	SSH_TTY	/dev/pts/38
string	STY	3697.WT.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
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	418
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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Parallel (threads) details

Task details

Global scope