Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20160928_164845_217
Start time	2016-09-28 16:48:45
Run time	22:50:40.832
Tasks executed	16
Tasks failed	1
Tasks failed names	spp rep1
Arguments*	[-title, ZF10, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $]
System*	sge
Cpus*	-1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20160928_164845_217/task.callpeak_spp.spp_rep1.line_54.id_25
thread_42	thread_Root	chipseq.bds.20160928_164845_217_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10 chipseq.bds.20160928_164845_217_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12 chipseq.bds.20160928_164845_217_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13 chipseq.bds.20160928_164845_217_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14 chipseq.bds.20160928_164845_217_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20160928_164845_217_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
thread_41	thread_Root	chipseq.bds.20160928_164845_217_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11 chipseq.bds.20160928_164845_217_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20160928_164845_217_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20160928_164845_217_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_ctl1.line_108.id_10
Name	bwa_aln ctl1
Thread	thread_42
PID	9635

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

Start	2016-09-28 16:48:47
End	2016-09-28 17:35:12
Elapsed	00:46:25
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/ZF10/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/ZF10/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--------------------
5706 (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... 33.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 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... 29.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 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... 30.08 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... 30.18 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... 30.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 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... 30.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.29 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... 30.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.00 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.37 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... 30.19 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.55 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... 29.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 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... 30.02 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.00 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... 30.06 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 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... 34.25 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.45 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... 29.88 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 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... 30.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.10 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.17 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.44 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.38 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... 30.27 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.39 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... 30.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.34 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... 30.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.40 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... 30.46 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.40 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... 31.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.88 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... 31.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.14 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... 30.45 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... 30.28 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... 30.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.67 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... 31.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.16 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... 31.58 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.15 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... 31.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 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... 29.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.65 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... 33.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.74 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... 28.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 8.44 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: 2774.591 sec; CPU: 2776.032 sec

Num	2
ID	task.align_bwa.bwa_aln_rep1.line_108.id_11
Name	bwa_aln rep1
Thread	thread_41
PID	9636

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

Start	2016-09-28 16:48:47
End	2016-09-28 18:46:29
Elapsed	01:57:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_allReps.fastq.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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--------------------
2910 (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] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.0% 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] 12058624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.35 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.1% 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] 33030144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.21 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.0% 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] 45350912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.91 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.18 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.43 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.21 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.1% 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] 74973184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.13 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 109973846 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/ZF10_allReps.fastq.gz
[main] Real time: 7052.173 sec; CPU: 25390.896 sec

Num	3
ID	task.align_bwa.bwa_sam_ctl1.line_140.id_12
Name	bwa_sam ctl1
Thread	thread_42
PID	9651

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

Start	2016-09-28 17:35:14
End	2016-09-28 17:49:02
Elapsed	00:13:47
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/ZF10/out/align/ctl1/mousePrimaryBCellInput.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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--------------------
4083 (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... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.40 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 7340032 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... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.70 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.41 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.72 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11534336 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... 0.34 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 11796480 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... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.83 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.48 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 13893632 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... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.36 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... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.95 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/ZF10/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 484.649 sec; CPU: 405.928 sec

Num	4
ID	task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
Name	dedup_bam_1 ctl1
Thread	thread_42
PID	9663

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

Start	2016-09-28 17:49:04
End	2016-09-28 17:53:17
Elapsed	00:04:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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--------------------
11825 (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	9670

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

Start	2016-09-28 17:53:18
End	2016-09-28 17:56:33
Elapsed	00:03:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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--------------------
4872 (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 17:57:35 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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 17:57:35 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 17:57:35	MarkDuplicates	Start of doWork freeMemory: 255390096; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 17:57:35	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 17:57:35	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 17:57:38	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:174,151,470
INFO	2016-09-28 17:57:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:40	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr2:135,780,411
INFO	2016-09-28 17:57:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:42	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    2s.  Last read position: chr3:122,530,375
INFO	2016-09-28 17:57:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:45	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    2s.  Last read position: chr4:135,044,888
INFO	2016-09-28 17:57:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:47	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    2s.  Last read position: chr5:135,067,778
INFO	2016-09-28 17:57:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:49	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    2s.  Last read position: chr6:144,681,933
INFO	2016-09-28 17:57:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:51	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr8:12,749,386
INFO	2016-09-28 17:57:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:55	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    3s.  Last read position: chr9:42,425,131
INFO	2016-09-28 17:57:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:00	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    5s.  Last read position: chr10:69,658,983
INFO	2016-09-28 17:58:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:04	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    3s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:58:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:06	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr13:6,026,344
INFO	2016-09-28 17:58:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:09	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    2s.  Last read position: chr14:54,434,282
INFO	2016-09-28 17:58:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:11	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr15:98,839,731
INFO	2016-09-28 17:58:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:13	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    2s.  Last read position: chr17:62,456,013
INFO	2016-09-28 17:58:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:16	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,585,732
INFO	2016-09-28 17:58:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:23	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 17:58:24	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1930416712; totalMemory: 2001534976; maxMemory: 3817799680
INFO	2016-09-28 17:58:24	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 17:58:24	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 17:58:24	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 17:58:27	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 17:58:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 802826712; totalMemory: 1767964672; maxMemory: 3817799680
INFO	2016-09-28 17:58:28	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 17:58:28	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 17:59:53	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 18:00:39	MarkDuplicates	Before output close freeMemory: 1865549088; totalMemory: 1878392832; maxMemory: 3817799680
INFO	2016-09-28 18:00:40	MarkDuplicates	After output close freeMemory: 1848639960; totalMemory: 1861484544; maxMemory: 3817799680
[Wed Sep 28 18:00:40 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.08 minutes.
Runtime.totalMemory()=1861484544

Num	6
ID	task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
Name	dedup_bam_2 ctl1
Thread	thread_42
PID	9674

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

Start	2016-09-28 17:56:34
End	2016-09-28 18:01:06
Elapsed	00:04:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/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--------------------
12889 (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	9682

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

Start	2016-09-28 18:01:08
End	2016-09-28 18:02:13
Elapsed	00:01:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/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/ZF10/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/ZF10/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--------------------
13745 (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	9701

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

Start	2016-09-28 18:46:31
End	2016-09-28 22:35:35
Elapsed	03:49:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_allReps.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.sai
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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--------------------
30349 (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] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.61 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.71 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.21 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.38 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.45 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.77 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.10 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.21 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.84 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.71 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.60 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.44 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.66 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.23 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.75 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.93 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.95 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.58 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.00 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.08 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.17 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.53 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.81 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.81 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.60 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.50 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.66 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.76 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.26 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.30 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.28 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.67 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.66 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.34 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.88 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.96 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.45 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.32 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.91 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.82 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.21 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.66 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.94 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.07 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.18 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.95 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.76 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.61 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.23 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 65.08 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 66.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 65.66 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.71 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 92.22 sec
[bwa_aln_core] refine gapped alignments... 14.84 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.44 sec
[bwa_aln_core] refine gapped alignments... 4.06 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.60 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 87.52 sec
[bwa_aln_core] refine gapped alignments... 14.31 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 78.83 sec
[bwa_aln_core] refine gapped alignments... 15.56 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 94.38 sec
[bwa_aln_core] refine gapped alignments... 14.85 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 93.34 sec
[bwa_aln_core] refine gapped alignments... 21.24 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 124.21 sec
[bwa_aln_core] refine gapped alignments... 23.30 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 87.32 sec
[bwa_aln_core] refine gapped alignments... 16.65 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 125.93 sec
[bwa_aln_core] refine gapped alignments... 3.85 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.79 sec
[bwa_aln_core] refine gapped alignments... 8.95 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.07 sec
[bwa_aln_core] refine gapped alignments... 8.05 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.52 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.65 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.34 sec
[bwa_aln_core] refine gapped alignments... 10.16 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 88.20 sec
[bwa_aln_core] refine gapped alignments... 11.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.05 sec
[bwa_aln_core] refine gapped alignments... 7.89 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.10 sec
[bwa_aln_core] refine gapped alignments... 4.30 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.30 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.27 sec
[bwa_aln_core] refine gapped alignments... 13.34 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.64 sec
[bwa_aln_core] refine gapped alignments... 10.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 102.19 sec
[bwa_aln_core] refine gapped alignments... 10.96 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 135.95 sec
[bwa_aln_core] refine gapped alignments... 15.67 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.88 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.19 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.30 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.53 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.04 sec
[bwa_aln_core] refine gapped alignments... 4.93 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 85.58 sec
[bwa_aln_core] refine gapped alignments... 13.76 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 94.92 sec
[bwa_aln_core] refine gapped alignments... 8.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.73 sec
[bwa_aln_core] refine gapped alignments... 14.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.72 sec
[bwa_aln_core] refine gapped alignments... 14.00 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 65.99 sec
[bwa_aln_core] refine gapped alignments... 13.24 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.13 sec
[bwa_aln_core] refine gapped alignments... 12.14 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.01 sec
[bwa_aln_core] refine gapped alignments... 8.69 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 65.03 sec
[bwa_aln_core] refine gapped alignments... 11.39 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.34 sec
[bwa_aln_core] refine gapped alignments... 30.12 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.1% 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... 0.48 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.6% 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... 0.50 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.84 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.12 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.64 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.03 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.11 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.48 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.11 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.27 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.47 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.86 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.23 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.82 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.73 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.90 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.32 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.30 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.82 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.04 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.02 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.65 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.67 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.86 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.80 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.09 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.03 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.81 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.15 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.41 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.37 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.08 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.00 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.84 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.21 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.78 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.57 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.75 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.72 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.55 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.04 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.82 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.07 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.80 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.08 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.49 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.77 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.91 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.84 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.73 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.40 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.50 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.70 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.93 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.37 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.68 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.81 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.54 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.72 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.92 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.88 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.31 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.37 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.25 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.21 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.56 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.45 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.38 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.70 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.40 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.73 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.24 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.11 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.19 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.76 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.28 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.72 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.80 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.39 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.14 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.76 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.45 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.51 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.10 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.87 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.16 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.34 sec
[bwa_aln_core] refine gapped alignments... 6.71 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.16 sec
[bwa_aln_core] refine gapped alignments... 8.07 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.66 sec
[bwa_aln_core] refine gapped alignments... 6.20 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.81 sec
[bwa_aln_core] refine gapped alignments... 8.95 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.48 sec
[bwa_aln_core] refine gapped alignments... 8.19 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 66.09 sec
[bwa_aln_core] refine gapped alignments... 12.64 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 94.29 sec
[bwa_aln_core] refine gapped alignments... 15.14 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.55 sec
[bwa_aln_core] refine gapped alignments... 11.57 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.73 sec
[bwa_aln_core] refine gapped alignments... 6.01 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.14 sec
[bwa_aln_core] refine gapped alignments... 10.34 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 68.02 sec
[bwa_aln_core] refine gapped alignments... 10.66 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.10 sec
[bwa_aln_core] refine gapped alignments... 14.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.10 sec
[bwa_aln_core] refine gapped alignments... 5.93 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.91 sec
[bwa_aln_core] refine gapped alignments... 13.59 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 89.37 sec
[bwa_aln_core] refine gapped alignments... 15.39 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 94.24 sec
[bwa_aln_core] refine gapped alignments... 14.65 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.89 sec
[bwa_aln_core] refine gapped alignments... 10.54 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.36 sec
[bwa_aln_core] refine gapped alignments... 12.64 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 87.06 sec
[bwa_aln_core] refine gapped alignments... 11.34 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.05 sec
[bwa_aln_core] refine gapped alignments... 10.56 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.59 sec
[bwa_aln_core] refine gapped alignments... 10.96 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.53 sec
[bwa_aln_core] refine gapped alignments... 13.30 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 104.75 sec
[bwa_aln_core] refine gapped alignments... 16.30 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 104.59 sec
[bwa_aln_core] refine gapped alignments... 3.95 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.11 sec
[bwa_aln_core] refine gapped alignments... 7.06 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.15 sec
[bwa_aln_core] refine gapped alignments... 9.97 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.24 sec
[bwa_aln_core] refine gapped alignments... 20.40 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.34 sec
[bwa_aln_core] refine gapped alignments... 4.63 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.72 sec
[bwa_aln_core] refine gapped alignments... 12.63 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 96.71 sec
[bwa_aln_core] refine gapped alignments... 24.96 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 127.86 sec
[bwa_aln_core] refine gapped alignments... 21.04 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 157.48 sec
[bwa_aln_core] refine gapped alignments... 10.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.71 sec
[bwa_aln_core] refine gapped alignments... 12.73 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.81 sec
[bwa_aln_core] refine gapped alignments... 14.21 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.27 sec
[bwa_aln_core] refine gapped alignments... 15.95 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.19 sec
[bwa_aln_core] refine gapped alignments... 16.12 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.80 sec
[bwa_aln_core] refine gapped alignments... 7.66 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.60 sec
[bwa_aln_core] refine gapped alignments... 15.49 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.39 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.27 sec
[bwa_aln_core] refine gapped alignments... 13.26 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.83 sec
[bwa_aln_core] refine gapped alignments... 10.67 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.95 sec
[bwa_aln_core] refine gapped alignments... 7.12 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 109973846 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/ZF10/out/align/rep1/ZF10_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_allReps.fastq.gz
[main] Real time: 13138.559 sec; CPU: 12770.652 sec

Num	9
ID	task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
Name	dedup_bam_1 rep1
Thread	thread_41
PID	9734

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

Start	2016-09-28 22:35:38
End	2016-09-28 22:43:23
Elapsed	00:07:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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--------------------
16681 (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	9737

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

Start	2016-09-28 22:43:24
End	2016-09-28 22:56:17
Elapsed	00:12:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.filt.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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--------------------
8033 (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 22:47:36 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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 22:47:36 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 22:47:36	MarkDuplicates	Start of doWork freeMemory: 255390264; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 22:47:36	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 22:47:36	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-28 22:47:36	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836463.13809573'.  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 22:47:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:55,373,157
INFO	2016-09-28 22:47:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:43	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    2s.  Last read position: chr1:92,652,404
INFO	2016-09-28 22:47:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:46	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr1:137,225,977
INFO	2016-09-28 22:47:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:47	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    1s.  Last read position: chr1:171,503,451
INFO	2016-09-28 22:47:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:49	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    1s.  Last read position: chr2:11,197,775
INFO	2016-09-28 22:47:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:52	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr2:34,970,327
INFO	2016-09-28 22:47:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:54	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    1s.  Last read position: chr2:75,487,928
INFO	2016-09-28 22:47:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:56	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    1s.  Last read position: chr2:117,955,100
INFO	2016-09-28 22:47:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:47:58	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    1s.  Last read position: chr2:148,426,740
INFO	2016-09-28 22:47:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:00	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    1s.  Last read position: chr2:168,867,221
INFO	2016-09-28 22:48:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:04	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    4s.  Last read position: chr3:42,731,077
INFO	2016-09-28 22:48:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:07	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    3s.  Last read position: chr3:88,467,279
INFO	2016-09-28 22:48:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:10	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    2s.  Last read position: chr3:115,615,597
INFO	2016-09-28 22:48:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:13	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr3:155,444,669
INFO	2016-09-28 22:48:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:18	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr4:47,381,608
INFO	2016-09-28 22:48:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:25	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    7s.  Last read position: chr4:103,124,568
INFO	2016-09-28 22:48:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:27	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    2s.  Last read position: chr4:130,014,890
INFO	2016-09-28 22:48:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:29	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chr4:148,903,031
INFO	2016-09-28 22:48:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:32	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    2s.  Last read position: chr5:31,218,198
INFO	2016-09-28 22:48:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:35	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    3s.  Last read position: chr5:73,655,682
INFO	2016-09-28 22:48:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:39	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    3s.  Last read position: chr5:114,773,415
INFO	2016-09-28 22:48:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:41	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    1s.  Last read position: chr5:136,781,998
INFO	2016-09-28 22:48:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:43	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    1s.  Last read position: chr6:22,642,354
INFO	2016-09-28 22:48:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:44	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    1s.  Last read position: chr6:63,139,473
INFO	2016-09-28 22:48:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:46	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    1s.  Last read position: chr6:100,547,331
INFO	2016-09-28 22:48:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:48	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    1s.  Last read position: chr6:134,793,454
INFO	2016-09-28 22:48:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:50	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    1s.  Last read position: chr7:25,956,926
INFO	2016-09-28 22:48:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:53	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr7:66,029,529
INFO	2016-09-28 22:48:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:56	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    2s.  Last read position: chr7:100,988,492
INFO	2016-09-28 22:48:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:48:58	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    2s.  Last read position: chr7:128,237,191
INFO	2016-09-28 22:48:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:06	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    7s.  Last read position: chr8:25,069,440
INFO	2016-09-28 22:49:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:08	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    2s.  Last read position: chr8:71,774,945
INFO	2016-09-28 22:49:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:11	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    2s.  Last read position: chr8:106,059,921
INFO	2016-09-28 22:49:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:13	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr9:8,025,090
INFO	2016-09-28 22:49:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:16	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    2s.  Last read position: chr9:50,554,190
INFO	2016-09-28 22:49:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:19	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    3s.  Last read position: chr9:73,073,223
INFO	2016-09-28 22:49:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:21	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    1s.  Last read position: chr9:108,517,672
INFO	2016-09-28 22:49:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:23	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    1s.  Last read position: chr10:19,510,475
INFO	2016-09-28 22:49:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:25	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    1s.  Last read position: chr10:61,625,891
INFO	2016-09-28 22:49:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:26	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    1s.  Last read position: chr10:85,224,232
INFO	2016-09-28 22:49:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:28	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    1s.  Last read position: chr10:122,992,065
INFO	2016-09-28 22:49:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:30	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    1s.  Last read position: chr11:29,714,506
INFO	2016-09-28 22:49:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:34	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    3s.  Last read position: chr11:61,221,533
INFO	2016-09-28 22:49:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:36	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:59s.  Time for last 1,000,000:    1s.  Last read position: chr11:80,146,709
INFO	2016-09-28 22:49:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:38	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    2s.  Last read position: chr11:99,466,347
INFO	2016-09-28 22:49:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:47	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    8s.  Last read position: chr11:116,581,562
INFO	2016-09-28 22:49:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:48	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    1s.  Last read position: chr12:36,715,696
INFO	2016-09-28 22:49:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:51	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    2s.  Last read position: chr12:84,674,405
INFO	2016-09-28 22:49:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:54	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:    3s.  Last read position: chr12:116,281,223
INFO	2016-09-28 22:49:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:49:56	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    2s.  Last read position: chr13:43,583,788
INFO	2016-09-28 22:49:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:00	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    3s.  Last read position: chr13:81,764,417
INFO	2016-09-28 22:50:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:01	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    1s.  Last read position: chr14:8,177,897
INFO	2016-09-28 22:50:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:03	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    1s.  Last read position: chr14:55,079,406
INFO	2016-09-28 22:50:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:05	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    1s.  Last read position: chr14:94,212,069
INFO	2016-09-28 22:50:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:07	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    1s.  Last read position: chr15:34,147,520
INFO	2016-09-28 22:50:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:08	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    1s.  Last read position: chr15:78,271,222
INFO	2016-09-28 22:50:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:10	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    1s.  Last read position: chr15:99,989,596
INFO	2016-09-28 22:50:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:12	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    1s.  Last read position: chr16:25,064,674
INFO	2016-09-28 22:50:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:14	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    1s.  Last read position: chr16:64,585,101
INFO	2016-09-28 22:50:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:18	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    3s.  Last read position: chr17:15,761,819
INFO	2016-09-28 22:50:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:26	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    7s.  Last read position: chr17:35,236,965
INFO	2016-09-28 22:50:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:28	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    2s.  Last read position: chr17:68,619,413
INFO	2016-09-28 22:50:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:30	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    2s.  Last read position: chr18:21,127,945
INFO	2016-09-28 22:50:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:32	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    2s.  Last read position: chr18:62,667,149
INFO	2016-09-28 22:50:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:35	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    2s.  Last read position: chr19:7,105,777
INFO	2016-09-28 22:50:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:37	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    2s.  Last read position: chr19:41,923,861
INFO	2016-09-28 22:50:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:40	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    2s.  Last read position: chrX:44,996,496
INFO	2016-09-28 22:50:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:42	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    2s.  Last read position: chrX:164,000,375
INFO	2016-09-28 22:50:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 22:50:42	MarkDuplicates	Read 68161793 records. 0 pairs never matched.
INFO	2016-09-28 22:50:45	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2808683288; totalMemory: 2895642624; maxMemory: 3817799680
INFO	2016-09-28 22:50:45	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 22:50:45	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 22:50:45	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 22:50:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 22:50:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1819434456; totalMemory: 2799108096; maxMemory: 3817799680
INFO	2016-09-28 22:50:59	MarkDuplicates	Marking 23245330 records as duplicates.
INFO	2016-09-28 22:50:59	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 22:52:21	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:22s.  Time for last 10,000,000:   82s.  Last read position: chr2:168,867,221
INFO	2016-09-28 22:53:43	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:43s.  Time for last 10,000,000:   81s.  Last read position: chr5:73,655,682
INFO	2016-09-28 22:55:05	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:05s.  Time for last 10,000,000:   82s.  Last read position: chr7:128,237,191
INFO	2016-09-28 22:56:26	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:27s.  Time for last 10,000,000:   81s.  Last read position: chr10:85,224,232
INFO	2016-09-28 22:57:50	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:51s.  Time for last 10,000,000:   83s.  Last read position: chr13:43,583,788
INFO	2016-09-28 22:59:14	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:15s.  Time for last 10,000,000:   84s.  Last read position: chr17:15,761,819
INFO	2016-09-28 23:00:24	MarkDuplicates	Before output close freeMemory: 2950810016; totalMemory: 2980642816; maxMemory: 3817799680
INFO	2016-09-28 23:00:24	MarkDuplicates	After output close freeMemory: 2950809176; totalMemory: 2980642816; maxMemory: 3817799680
[Wed Sep 28 23:00:24 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 12.80 minutes.
Runtime.totalMemory()=2980642816

Num	11
ID	task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
Name	dedup_bam_2 rep1
Thread	thread_41
PID	9739

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

Start	2016-09-28 22:56:18
End	2016-09-28 23:14:05
Elapsed	00:17:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.flagstat.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/out/qc/rep1/ZF10_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--------------------
27781 (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	9744

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

Start	2016-09-28 23:14:07
End	2016-09-28 23:15:52
Elapsed	00:01:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.bam
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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--------------------
8302 (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	13
ID	task.postalign_bed.subsample_tag_rep1.line_41.id_22
Name	subsample_tag rep1
Thread	thread_41
PID	9746

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

Start	2016-09-28 23:15:54
End	2016-09-28 23:16:58
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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--------------------
8391 (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	14
ID	task.postalign_bed.spr_rep1.line_247.id_23
Name	spr rep1
Thread	thread_41
PID	9747

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

Start	2016-09-28 23:15:55
End	2016-09-28 23:17:54
Elapsed	00:01:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr2/ZF10_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/ZF10/out/align/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr2/ZF10_allReps.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/pseudo_reps/rep1/pr1/ZF10_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--------------------
8390 (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	15
ID	task.postalign_bed.xcor_rep1.line_205.id_24
Name	xcor rep1
Thread	thread_41
PID	9748

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

Start	2016-09-28 23:17:55
End	2016-09-28 23:26:19
Elapsed	00:08:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.15M.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_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--------------------
38878 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_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/ZF10/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/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/qc/rep1/ZF10_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9748.1.q/RtmpOObLdz/ZF10_allReps.nodup.15M.tagAlign98485220793
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1980801 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.263883290986752 
Top 3 estimates for fragment length 120 
Window half size 445 
Phantom peak location 55 
Phantom peak Correlation 0.2534412 
Normalized Strand cross-correlation coefficient (NSC) 1.332205 
Relative Strand Cross correlation Coefficient (RSC) 1.188619 
Phantom Peak Quality Tag 1 
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	9754

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

Start	2016-09-28 23:26:20
End	2016-09-28 23:26:20
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1 -speak=120 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_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/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_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

 
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
  
--------------------Stdout--------------------
8816 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 120 
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/ZF10/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/peak/spp/rep1/ZF10_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/ZF10/out/align/rep1/ZF10_allReps.nodup.tagAlign.gz 
opened /tmp/9754.1.q/RtmpPkvDyg/ZF10_allReps.nodup.tagAlign22b27b6971bd
done. read 44916463 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9754.1.q/RtmpPkvDyg/mousePrimaryBCellInput.nodup.tagAlign22b237caf314
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.387795 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.516905583538379 
Top 3 estimates for fragment length 120 
Window half size 445 
Phantom peak location 55 
Phantom peak Correlation 0.496508 
Normalized Strand cross-correlation coefficient (NSC) 1.332935 
Relative Strand Cross correlation Coefficient (RSC) 1.187627 
Phantom Peak Quality Tag 1 
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= 0.4687107  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 2.133512  
 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZF10, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF10/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF10_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/ZF10
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/ZF10
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	5368.ZF10.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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