chipseq.bds.20160928_164720_431/task.callpeak_spp.spp_rep1.line_54.id_25
chipseq.bds.20160928_164720_431/task.callpeak_idr.idr_final_qc.line_205.id_26
chipseq.bds.20160928_164720_431/task.graphviz.report.line_97.id_27
chipseq.bds.20160928_164720_431/task.report.pdf2png.line_324.id_32
 

 chipseq.bds.20160928_164720_431_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11
chipseq.bds.20160928_164720_431_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20160928_164720_431_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 chipseq.bds.20160928_164720_431_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10
chipseq.bds.20160928_164720_431_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20160928_164720_431_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
chipseq.bds.20160928_164720_431_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
chipseq.bds.20160928_164720_431_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
chipseq.bds.20160928_164720_431_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
 

 
# 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/ZF3/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--------------------
4365 (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... 26.74 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... 26.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 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] 1310720 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... 0.03 sec
[bwa_aln_core] 1572864 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] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.71 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... 35.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.62 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... 31.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.30 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... 31.20 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... 31.34 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... 32.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.22 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... 31.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.58 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... 33.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.07 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... 33.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.24 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.11 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... 31.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 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] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.25 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... 30.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.42 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... 30.50 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... 0.03 sec
[bwa_aln_core] 12582912 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... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.57 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... 30.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.65 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... 30.54 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... 30.73 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... 30.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.31 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... 33.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.11 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... 32.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 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... 31.06 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... 30.68 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... 30.85 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... 30.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.77 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... 31.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.98 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... 31.33 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... 30.88 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... 30.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.10 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... 30.93 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... 31.03 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... 30.59 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... 30.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.54 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... 32.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.61 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... 31.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.37 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... 31.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.46 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 23141323 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 2857.218 sec; CPU: 2858.696 sec

 

 
# 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/ZF3_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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--------------------
11853 (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] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.84 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.48 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... 54.51 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... 55.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.53 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... 56.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.92 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... 60.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.01 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... 59.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.51 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.91 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... 61.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.74 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... 60.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.78 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.34 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... 57.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.27 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.24 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... 60.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.92 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... 59.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.44 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... 59.47 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... 57.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.36 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... 56.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.55 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... 60.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.31 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... 71.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 8.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 4.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46923776 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... 0.05 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.24 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 7.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 11.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 13.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 8.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 11.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 10.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 7.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 5.6% 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] 64749568 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 7.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 13.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 15.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 14.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 9.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 12.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 12.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 9.1% 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] 77332480 sequences have been processed.
[bwa_read_seq] 7.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 4.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 6.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 12.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 12.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 14.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 5.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 4.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.24 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... 60.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 12.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 9.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 7.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 5.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 6.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 10.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 13.0% 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] 100401152 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 10.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 8.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 7.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 5.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.9% 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] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 14.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 15.0% 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] 106430464 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 11.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.52 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 8.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 6.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 114675283 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/ZF3_allReps.fastq.gz
[main] Real time: 7976.757 sec; CPU: 29831.816 sec

 

 
# 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/ZF3/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/ZF3/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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--------------------
41482 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.50 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.61 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... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.22 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.81 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.30 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.56 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.35 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.44 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.61 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.00 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.95 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.21 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/ZF3/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 618.610 sec; CPU: 529.772 sec

 

 
# 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/ZF3/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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/ZF3/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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--------------------
4695 (process ID) old priority 0, new priority 10

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

 

 
# 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/ZF3/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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/ZF3/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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--------------------
12983 (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 17:56:58 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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 17:56:58 PDT 2016] Executing as imk1@surya on Linux 4.2.0-27-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-28 17:56:58	MarkDuplicates	Start of doWork freeMemory: 255390120; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 17:56:58	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 17:56:58	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 17:57:03	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr1:174,151,470
INFO	2016-09-28 17:57:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:06	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    3s.  Last read position: chr2:135,780,411
INFO	2016-09-28 17:57:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:09	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    3s.  Last read position: chr3:122,530,375
INFO	2016-09-28 17:57:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:12	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    2s.  Last read position: chr4:135,044,888
INFO	2016-09-28 17:57:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:15	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    2s.  Last read position: chr5:135,067,778
INFO	2016-09-28 17:57:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:19	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    4s.  Last read position: chr6:144,681,933
INFO	2016-09-28 17:57:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:24	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    4s.  Last read position: chr8:12,749,386
INFO	2016-09-28 17:57:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:26	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    2s.  Last read position: chr9:42,425,131
INFO	2016-09-28 17:57:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:29	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    2s.  Last read position: chr10:69,658,983
INFO	2016-09-28 17:57:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:33	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    4s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:57:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:36	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr13:6,026,344
INFO	2016-09-28 17:57:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:38	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr14:54,434,282
INFO	2016-09-28 17:57:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:41	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    2s.  Last read position: chr15:98,839,731
INFO	2016-09-28 17:57:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:46	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    4s.  Last read position: chr17:62,456,013
INFO	2016-09-28 17:57:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:48	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,585,732
INFO	2016-09-28 17:57:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:57:55	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 17:57:56	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2524303096; totalMemory: 2610626560; maxMemory: 3817799680
INFO	2016-09-28 17:57:56	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 17:57:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 17:57:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 17:58:00	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 17:58:00	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1980709272; totalMemory: 2956656640; maxMemory: 3817799680
INFO	2016-09-28 17:58:00	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 17:58:00	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 17:59:24	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:23s.  Time for last 10,000,000:   83s.  Last read position: chr11:86,536,377
INFO	2016-09-28 18:00:11	MarkDuplicates	Before output close freeMemory: 2928380320; totalMemory: 2956460032; maxMemory: 3817799680
INFO	2016-09-28 18:00:11	MarkDuplicates	After output close freeMemory: 2956035672; totalMemory: 2984116224; maxMemory: 3817799680
[Wed Sep 28 18:00:12 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.23 minutes.
Runtime.totalMemory()=2984116224

 

 
# 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/ZF3/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/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/ZF3/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--------------------
13602 (process ID) old priority 0, new priority 10

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

 

 
# 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/ZF3/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/ZF3/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--------------------
5631 (process ID) old priority 0, new priority 10

Waiting for 27 seconds.

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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF3_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_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--------------------
6743 (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] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.20 sec
[bwa_aln_core] refine gapped alignments... 5.83 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.48 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.55 sec
[bwa_aln_core] refine gapped alignments... 5.85 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.26 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.83 sec
[bwa_aln_core] refine gapped alignments... 3.72 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.12 sec
[bwa_aln_core] refine gapped alignments... 3.74 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.89 sec
[bwa_aln_core] refine gapped alignments... 4.80 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.24 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.60 sec
[bwa_aln_core] refine gapped alignments... 5.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.35 sec
[bwa_aln_core] refine gapped alignments... 4.20 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.11 sec
[bwa_aln_core] refine gapped alignments... 4.14 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.42 sec
[bwa_aln_core] refine gapped alignments... 3.97 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.66 sec
[bwa_aln_core] refine gapped alignments... 4.67 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.00 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.18 sec
[bwa_aln_core] refine gapped alignments... 1.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.96 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.49 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.77 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.88 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.35 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.40 sec
[bwa_aln_core] refine gapped alignments... 4.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.03 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.77 sec
[bwa_aln_core] refine gapped alignments... 3.65 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.14 sec
[bwa_aln_core] refine gapped alignments... 4.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.25 sec
[bwa_aln_core] refine gapped alignments... 3.84 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.94 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.62 sec
[bwa_aln_core] refine gapped alignments... 4.10 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.86 sec
[bwa_aln_core] refine gapped alignments... 4.53 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.00 sec
[bwa_aln_core] refine gapped alignments... 4.19 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.28 sec
[bwa_aln_core] refine gapped alignments... 5.68 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.95 sec
[bwa_aln_core] refine gapped alignments... 5.02 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.70 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.70 sec
[bwa_aln_core] refine gapped alignments... 4.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.70 sec
[bwa_aln_core] refine gapped alignments... 4.24 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.82 sec
[bwa_aln_core] refine gapped alignments... 4.92 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.63 sec
[bwa_aln_core] refine gapped alignments... 2.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.37 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 9437184 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... 2.29 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.04 sec
[bwa_aln_core] refine gapped alignments... 3.30 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.53 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.09 sec
[bwa_aln_core] refine gapped alignments... 4.75 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.25 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.19 sec
[bwa_aln_core] refine gapped alignments... 5.87 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.47 sec
[bwa_aln_core] refine gapped alignments... 5.71 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.20 sec
[bwa_aln_core] refine gapped alignments... 4.13 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.47 sec
[bwa_aln_core] refine gapped alignments... 3.01 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.82 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.59 sec
[bwa_aln_core] refine gapped alignments... 4.92 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.03 sec
[bwa_aln_core] refine gapped alignments... 3.06 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.10 sec
[bwa_aln_core] refine gapped alignments... 5.75 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.37 sec
[bwa_aln_core] refine gapped alignments... 4.65 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.13 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.20 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.75 sec
[bwa_aln_core] refine gapped alignments... 5.07 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.35 sec
[bwa_aln_core] refine gapped alignments... 4.66 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.31 sec
[bwa_aln_core] refine gapped alignments... 4.56 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.23 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.80 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.15 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.95 sec
[bwa_aln_core] refine gapped alignments... 1.63 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.53 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.67 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.00 sec
[bwa_aln_core] refine gapped alignments... 4.86 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.76 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.27 sec
[bwa_aln_core] refine gapped alignments... 4.72 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.50 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.29 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.04 sec
[bwa_aln_core] refine gapped alignments... 4.87 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.60 sec
[bwa_aln_core] refine gapped alignments... 4.06 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.56 sec
[bwa_aln_core] refine gapped alignments... 4.68 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.61 sec
[bwa_aln_core] refine gapped alignments... 4.74 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.66 sec
[bwa_aln_core] refine gapped alignments... 4.94 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.08 sec
[bwa_aln_core] refine gapped alignments... 4.96 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.89 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.31 sec
[bwa_aln_core] refine gapped alignments... 3.90 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.97 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.58 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.18 sec
[bwa_aln_core] refine gapped alignments... 3.68 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.43 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.65 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.95 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.39 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.82 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.35 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.89 sec
[bwa_aln_core] refine gapped alignments... 5.57 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.87 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.00 sec
[bwa_aln_core] refine gapped alignments... 3.02 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.16 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.19 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.08 sec
[bwa_aln_core] refine gapped alignments... 3.97 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.04 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.65 sec
[bwa_aln_core] refine gapped alignments... 2.98 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.16 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.95 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24379392 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... 1.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.85 sec
[bwa_aln_core] refine gapped alignments... 4.29 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.25 sec
[bwa_aln_core] refine gapped alignments... 4.53 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.38 sec
[bwa_aln_core] refine gapped alignments... 4.71 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.30 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.69 sec
[bwa_aln_core] refine gapped alignments... 4.86 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.54 sec
[bwa_aln_core] refine gapped alignments... 4.95 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.55 sec
[bwa_aln_core] refine gapped alignments... 3.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.62 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.53 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.44 sec
[bwa_aln_core] refine gapped alignments... 5.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.18 sec
[bwa_aln_core] refine gapped alignments... 5.06 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.19 sec
[bwa_aln_core] refine gapped alignments... 3.82 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 27787264 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... 4.08 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.87 sec
[bwa_aln_core] refine gapped alignments... 4.87 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.96 sec
[bwa_aln_core] refine gapped alignments... 5.96 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.93 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.47 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.32 sec
[bwa_aln_core] refine gapped alignments... 3.07 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.18 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.52 sec
[bwa_aln_core] refine gapped alignments... 4.15 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.50 sec
[bwa_aln_core] refine gapped alignments... 5.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.73 sec
[bwa_aln_core] refine gapped alignments... 2.78 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.57 sec
[bwa_aln_core] refine gapped alignments... 1.94 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.96 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.42 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.60 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.54 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.13 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.78 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.00 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.08 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.09 sec
[bwa_aln_core] refine gapped alignments... 1.66 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.26 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.15 sec
[bwa_aln_core] refine gapped alignments... 1.79 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.59 sec
[bwa_aln_core] refine gapped alignments... 3.17 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.60 sec
[bwa_aln_core] refine gapped alignments... 3.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.54 sec
[bwa_aln_core] refine gapped alignments... 3.22 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.51 sec
[bwa_aln_core] refine gapped alignments... 3.19 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.01 sec
[bwa_aln_core] refine gapped alignments... 3.14 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.76 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.57 sec
[bwa_aln_core] refine gapped alignments... 3.24 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.83 sec
[bwa_aln_core] refine gapped alignments... 3.56 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.34 sec
[bwa_aln_core] refine gapped alignments... 2.18 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.25 sec
[bwa_aln_core] refine gapped alignments... 2.17 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.46 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.09 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.64 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.50 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.13 sec
[bwa_aln_core] refine gapped alignments... 2.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.54 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.95 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.61 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.43 sec
[bwa_aln_core] refine gapped alignments... 3.90 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.42 sec
[bwa_aln_core] refine gapped alignments... 3.64 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.43 sec
[bwa_aln_core] refine gapped alignments... 3.64 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.87 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.63 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.15 sec
[bwa_aln_core] refine gapped alignments... 3.73 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.09 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.81 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.28 sec
[bwa_aln_core] refine gapped alignments... 4.15 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.37 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.83 sec
[bwa_aln_core] refine gapped alignments... 4.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.01 sec
[bwa_aln_core] refine gapped alignments... 3.59 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.03 sec
[bwa_aln_core] refine gapped alignments... 3.75 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.03 sec
[bwa_aln_core] refine gapped alignments... 3.71 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.27 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.36 sec
[bwa_aln_core] refine gapped alignments... 3.71 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.90 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.38 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.94 sec
[bwa_aln_core] refine gapped alignments... 4.08 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.26 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 4.26 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 8.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.45 sec
[bwa_aln_core] refine gapped alignments... 4.27 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.96 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 4.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.46 sec
[bwa_aln_core] refine gapped alignments... 3.76 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.42 sec
[bwa_aln_core] refine gapped alignments... 3.69 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.14 sec
[bwa_aln_core] refine gapped alignments... 4.02 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.02 sec
[bwa_aln_core] refine gapped alignments... 3.68 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.89 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.72 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.06 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.86 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.61 sec
[bwa_aln_core] refine gapped alignments... 4.25 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.88 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.25 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.14 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.61 sec
[bwa_aln_core] refine gapped alignments... 4.10 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.50 sec
[bwa_aln_core] refine gapped alignments... 4.12 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.85 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.21 sec
[bwa_aln_core] refine gapped alignments... 4.96 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 7.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.90 sec
[bwa_aln_core] refine gapped alignments... 4.56 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 11.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.96 sec
[bwa_aln_core] refine gapped alignments... 4.15 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 13.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.57 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.66 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.67 sec
[bwa_aln_core] refine gapped alignments... 4.32 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.37 sec
[bwa_aln_core] refine gapped alignments... 4.15 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.55 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.86 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 8.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.45 sec
[bwa_aln_core] refine gapped alignments... 4.15 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.88 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.41 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.43 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.20 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.19 sec
[bwa_aln_core] refine gapped alignments... 3.91 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.18 sec
[bwa_aln_core] refine gapped alignments... 4.56 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.91 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.34 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.02 sec
[bwa_aln_core] refine gapped alignments... 3.33 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.44 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.94 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.19 sec
[bwa_aln_core] refine gapped alignments... 4.02 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.39 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.47 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.47 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.52 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.31 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.80 sec
[bwa_aln_core] refine gapped alignments... 4.09 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.09 sec
[bwa_aln_core] refine gapped alignments... 3.78 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.31 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.50 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.20 sec
[bwa_aln_core] refine gapped alignments... 4.06 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 11.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.49 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.88 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.44 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.77 sec
[bwa_aln_core] refine gapped alignments... 4.78 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.48 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.98 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.55 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.78 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.18 sec
[bwa_aln_core] refine gapped alignments... 4.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.16 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.81 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.70 sec
[bwa_aln_core] refine gapped alignments... 4.09 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.63 sec
[bwa_aln_core] refine gapped alignments... 4.30 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.35 sec
[bwa_aln_core] refine gapped alignments... 4.06 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.66 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.54 sec
[bwa_aln_core] refine gapped alignments... 4.78 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.57 sec
[bwa_aln_core] refine gapped alignments... 4.18 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.44 sec
[bwa_aln_core] refine gapped alignments... 4.09 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.38 sec
[bwa_aln_core] refine gapped alignments... 4.10 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.70 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.72 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.66 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.88 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.42 sec
[bwa_aln_core] refine gapped alignments... 4.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.69 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 10.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.71 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.51 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 7.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.89 sec
[bwa_aln_core] refine gapped alignments... 4.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.38 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.66 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.78 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.16 sec
[bwa_aln_core] refine gapped alignments... 4.03 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.46 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.27 sec
[bwa_aln_core] refine gapped alignments... 4.37 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.13 sec
[bwa_aln_core] refine gapped alignments... 4.12 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.06 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.17 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.11 sec
[bwa_aln_core] refine gapped alignments... 4.28 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.08 sec
[bwa_aln_core] refine gapped alignments... 5.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.36 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.54 sec
[bwa_aln_core] refine gapped alignments... 4.14 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.41 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.26 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.70 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 7.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.00 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 11.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.63 sec
[bwa_aln_core] refine gapped alignments... 4.97 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 13.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.00 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.07 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 15.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.69 sec
[bwa_aln_core] refine gapped alignments... 3.64 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 14.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.97 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.80 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.49 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 9.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.53 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.99 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.68 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.83 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.11 sec
[bwa_aln_core] refine gapped alignments... 2.75 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.40 sec
[bwa_aln_core] refine gapped alignments... 3.52 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.73 sec
[bwa_aln_core] refine gapped alignments... 3.81 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.23 sec
[bwa_aln_core] refine gapped alignments... 5.79 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.39 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.65 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.30 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.05 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.63 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.85 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.80 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.39 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.12 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.26 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 9.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.59 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 12.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.05 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.55 sec
[bwa_aln_core] refine gapped alignments... 4.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.88 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 12.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.08 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.02 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 9.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.47 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 7.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.95 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.50 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 4.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.98 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.76 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.71 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.86 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.76 sec
[bwa_aln_core] refine gapped alignments... 1.96 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.40 sec
[bwa_aln_core] refine gapped alignments... 3.68 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.21 sec
[bwa_aln_core] refine gapped alignments... 3.68 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.71 sec
[bwa_aln_core] refine gapped alignments... 3.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.52 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.08 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.23 sec
[bwa_aln_core] refine gapped alignments... 6.03 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.07 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.94 sec
[bwa_aln_core] refine gapped alignments... 3.96 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.45 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.99 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 6.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.54 sec
[bwa_aln_core] refine gapped alignments... 3.69 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.74 sec
[bwa_aln_core] refine gapped alignments... 3.19 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 12.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.20 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.21 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 12.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.03 sec
[bwa_aln_core] refine gapped alignments... 2.67 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 11.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.74 sec
[bwa_aln_core] refine gapped alignments... 3.64 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.15 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.10 sec
[bwa_aln_core] refine gapped alignments... 3.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.47 sec
[bwa_aln_core] refine gapped alignments... 3.83 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.50 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.47 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.28 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.14 sec
[bwa_aln_core] refine gapped alignments... 3.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.06 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.87 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.97 sec
[bwa_aln_core] refine gapped alignments... 5.66 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.86 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.12 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.80 sec
[bwa_aln_core] refine gapped alignments... 5.67 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.14 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.27 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.90 sec
[bwa_aln_core] refine gapped alignments... 3.88 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.44 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 10.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.26 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.40 sec
[bwa_aln_core] refine gapped alignments... 3.79 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 14.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.22 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 14.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.56 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.74 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.74 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.22 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.83 sec
[bwa_aln_core] refine gapped alignments... 4.57 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 5.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.85 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 4.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.30 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.34 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.10 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.76 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.54 sec
[bwa_aln_core] refine gapped alignments... 3.00 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.97 sec
[bwa_aln_core] refine gapped alignments... 1.94 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.02 sec
[bwa_aln_core] refine gapped alignments... 3.22 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.43 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.90 sec
[bwa_aln_core] refine gapped alignments... 3.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.72 sec
[bwa_aln_core] refine gapped alignments... 4.79 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.65 sec
[bwa_aln_core] refine gapped alignments... 4.54 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.04 sec
[bwa_aln_core] refine gapped alignments... 5.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.16 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.63 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.29 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 13.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.80 sec
[bwa_aln_core] refine gapped alignments... 3.65 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 13.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.14 sec
[bwa_aln_core] refine gapped alignments... 3.65 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 12.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.06 sec
[bwa_aln_core] refine gapped alignments... 5.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 9.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.81 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 7.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.14 sec
[bwa_aln_core] refine gapped alignments... 4.22 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 5.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.12 sec
[bwa_aln_core] refine gapped alignments... 3.75 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.49 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.48 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.91 sec
[bwa_aln_core] refine gapped alignments... 3.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.38 sec
[bwa_aln_core] refine gapped alignments... 2.85 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.36 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.80 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.57 sec
[bwa_aln_core] refine gapped alignments... 2.78 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.61 sec
[bwa_aln_core] refine gapped alignments... 3.74 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.31 sec
[bwa_aln_core] refine gapped alignments... 3.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.17 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.96 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.79 sec
[bwa_aln_core] refine gapped alignments... 3.25 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 6.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.26 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 10.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.60 sec
[bwa_aln_core] refine gapped alignments... 3.29 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 13.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.88 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.64 sec
[bwa_aln_core] refine gapped alignments... 3.00 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.94 sec
[bwa_aln_core] refine gapped alignments... 3.10 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 10.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.18 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 8.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.57 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 7.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.42 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 5.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.81 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.73 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.25 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.61 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.46 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.45 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.44 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.41 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.61 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.39 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.51 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.69 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.78 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.95 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 14.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.69 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 15.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.86 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 14.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.81 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.92 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 11.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.86 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 7.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.92 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.93 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.19 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.14 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.40 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.18 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.93 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.99 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.52 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.00 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.00 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.84 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.80 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.17 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 13.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 13.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.98 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 11.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.79 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.10 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 8.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.52 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 6.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.61 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.78 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.64 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.69 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.87 sec
[bwa_aln_core] refine gapped alignments... 0.26 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 114675283 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/ZF3/out/align/rep1/ZF3_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF3_allReps.fastq.gz
[main] Real time: 13902.542 sec; CPU: 13685.684 sec

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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/ZF3/out/align/rep1/ZF3_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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--------------------
35315 (process ID) old priority 0, new priority 10

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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_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--------------------
8189 (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 23:11:22 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_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 23:11:22 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 23:11:22	MarkDuplicates	Start of doWork freeMemory: 255390312; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 23:11:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 23:11:22	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-28 23:11:22	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836473.22876510'.  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 23:11:26	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr1:49,496,004
INFO	2016-09-28 23:11:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:30	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    3s.  Last read position: chr1:86,442,332
INFO	2016-09-28 23:11:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:34	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    3s.  Last read position: chr1:130,854,309
INFO	2016-09-28 23:11:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:36	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    2s.  Last read position: chr1:160,830,010
INFO	2016-09-28 23:11:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:38	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr1:189,922,280
INFO	2016-09-28 23:11:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:41	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    2s.  Last read position: chr2:28,304,903
INFO	2016-09-28 23:11:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:45	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    4s.  Last read position: chr2:58,008,421
INFO	2016-09-28 23:11:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:49	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    3s.  Last read position: chr2:92,824,619
INFO	2016-09-28 23:11:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:51	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    2s.  Last read position: chr2:125,782,672
INFO	2016-09-28 23:11:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:55	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    4s.  Last read position: chr2:155,595,761
INFO	2016-09-28 23:11:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:11:58	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr2:181,307,198
INFO	2016-09-28 23:11:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:00	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr3:52,621,542
INFO	2016-09-28 23:12:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:02	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr3:89,218,854
INFO	2016-09-28 23:12:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:05	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    2s.  Last read position: chr3:118,158,759
INFO	2016-09-28 23:12:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:10	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr3:154,653,249
INFO	2016-09-28 23:12:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:18	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    8s.  Last read position: chr4:44,695,467
INFO	2016-09-28 23:12:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:20	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    2s.  Last read position: chr4:88,522,816
INFO	2016-09-28 23:12:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:23	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    2s.  Last read position: chr4:123,353,968
INFO	2016-09-28 23:12:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:26	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chr4:141,065,344
INFO	2016-09-28 23:12:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:28	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chr5:23,712,792
INFO	2016-09-28 23:12:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:32	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    3s.  Last read position: chr5:62,779,417
INFO	2016-09-28 23:12:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:33	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    1s.  Last read position: chr5:103,688,134
INFO	2016-09-28 23:12:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:35	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    2s.  Last read position: chr5:125,003,058
INFO	2016-09-28 23:12:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:37	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    1s.  Last read position: chr5:149,221,747
INFO	2016-09-28 23:12:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:39	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    1s.  Last read position: chr6:40,925,579
INFO	2016-09-28 23:12:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:43	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    3s.  Last read position: chr6:83,162,564
INFO	2016-09-28 23:12:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:44	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    1s.  Last read position: chr6:115,008,942
INFO	2016-09-28 23:12:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:46	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    2s.  Last read position: chr6:145,622,153
INFO	2016-09-28 23:12:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:49	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    2s.  Last read position: chr7:35,189,329
INFO	2016-09-28 23:12:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:51	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    2s.  Last read position: chr7:77,870,167
INFO	2016-09-28 23:12:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:12:59	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    7s.  Last read position: chr7:109,616,384
INFO	2016-09-28 23:12:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:01	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    2s.  Last read position: chr7:135,735,803
INFO	2016-09-28 23:13:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:04	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    2s.  Last read position: chr8:31,110,537
INFO	2016-09-28 23:13:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:06	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    1s.  Last read position: chr8:72,396,526
INFO	2016-09-28 23:13:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:07	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    1s.  Last read position: chr8:106,693,097
INFO	2016-09-28 23:13:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:09	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    1s.  Last read position: chr9:7,772,965
INFO	2016-09-28 23:13:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:11	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    1s.  Last read position: chr9:44,880,907
INFO	2016-09-28 23:13:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:13	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    1s.  Last read position: chr9:69,673,576
INFO	2016-09-28 23:13:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:15	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    1s.  Last read position: chr9:104,204,270
INFO	2016-09-28 23:13:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:18	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    3s.  Last read position: chr10:11,355,165
INFO	2016-09-28 23:13:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:20	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    2s.  Last read position: chr10:48,038,232
INFO	2016-09-28 23:13:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:22	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    2s.  Last read position: chr10:79,938,939
INFO	2016-09-28 23:13:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:25	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    2s.  Last read position: chr10:110,252,840
INFO	2016-09-28 23:13:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:27	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    2s.  Last read position: chr11:12,417,437
INFO	2016-09-28 23:13:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:29	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    2s.  Last read position: chr11:50,443,255
INFO	2016-09-28 23:13:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:36	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    6s.  Last read position: chr11:73,169,408
INFO	2016-09-28 23:13:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:38	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    1s.  Last read position: chr11:95,259,422
INFO	2016-09-28 23:13:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:40	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    2s.  Last read position: chr11:114,383,390
INFO	2016-09-28 23:13:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:43	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    2s.  Last read position: chr12:27,862,330
INFO	2016-09-28 23:13:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:45	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    1s.  Last read position: chr12:73,989,795
INFO	2016-09-28 23:13:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:47	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    2s.  Last read position: chr12:104,419,396
INFO	2016-09-28 23:13:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:49	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    1s.  Last read position: chr13:23,999,750
INFO	2016-09-28 23:13:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:50	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    1s.  Last read position: chr13:53,685,650
INFO	2016-09-28 23:13:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:52	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    1s.  Last read position: chr13:94,484,809
INFO	2016-09-28 23:13:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:54	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    1s.  Last read position: chr14:19,962,212
INFO	2016-09-28 23:13:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:58	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    3s.  Last read position: chr14:56,381,212
INFO	2016-09-28 23:13:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:13:59	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    1s.  Last read position: chr14:92,316,341
INFO	2016-09-28 23:13:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:01	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    2s.  Last read position: chr15:18,650,282
INFO	2016-09-28 23:14:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:04	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr15:66,559,642
INFO	2016-09-28 23:14:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:06	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    2s.  Last read position: chr15:89,623,977
INFO	2016-09-28 23:14:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:14	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    7s.  Last read position: chr16:15,888,087
INFO	2016-09-28 23:14:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:16	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    1s.  Last read position: chr16:44,034,155
INFO	2016-09-28 23:14:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:18	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    2s.  Last read position: chr16:91,044,531
INFO	2016-09-28 23:14:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:20	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    2s.  Last read position: chr17:26,713,049
INFO	2016-09-28 23:14:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:23	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    2s.  Last read position: chr17:46,585,514
INFO	2016-09-28 23:14:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:25	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    1s.  Last read position: chr17:81,882,090
INFO	2016-09-28 23:14:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:27	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    1s.  Last read position: chr18:32,879,488
INFO	2016-09-28 23:14:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:28	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    1s.  Last read position: chr18:67,547,210
INFO	2016-09-28 23:14:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:30	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    1s.  Last read position: chr19:10,908,074
INFO	2016-09-28 23:14:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:32	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    2s.  Last read position: chr19:43,771,650
INFO	2016-09-28 23:14:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:34	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    1s.  Last read position: chrX:49,410,743
INFO	2016-09-28 23:14:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:36	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    1s.  Last read position: chrX:157,903,340
INFO	2016-09-28 23:14:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 23:14:36	MarkDuplicates	Read 72272248 records. 0 pairs never matched.
INFO	2016-09-28 23:14:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2122661760; totalMemory: 2209611776; maxMemory: 3817799680
INFO	2016-09-28 23:14:40	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 23:14:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 23:14:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 23:14:54	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 23:14:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2226339488; totalMemory: 3206283264; maxMemory: 3817799680
INFO	2016-09-28 23:14:56	MarkDuplicates	Marking 41316560 records as duplicates.
INFO	2016-09-28 23:14:56	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 23:16:16	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:20s.  Time for last 10,000,000:   80s.  Last read position: chr2:155,595,761
INFO	2016-09-28 23:17:36	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:39s.  Time for last 10,000,000:   79s.  Last read position: chr5:23,712,792
INFO	2016-09-28 23:18:55	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:03:58s.  Time for last 10,000,000:   79s.  Last read position: chr7:77,870,167
INFO	2016-09-28 23:20:16	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:19s.  Time for last 10,000,000:   80s.  Last read position: chr10:11,355,165
INFO	2016-09-28 23:21:39	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:42s.  Time for last 10,000,000:   82s.  Last read position: chr12:73,989,795
INFO	2016-09-28 23:22:58	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:02s.  Time for last 10,000,000:   79s.  Last read position: chr15:89,623,977
INFO	2016-09-28 23:24:18	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:21s.  Time for last 10,000,000:   79s.  Last read position: chr19:43,771,650
INFO	2016-09-28 23:24:36	MarkDuplicates	Before output close freeMemory: 3270530192; totalMemory: 3300458496; maxMemory: 3817799680
INFO	2016-09-28 23:24:37	MarkDuplicates	After output close freeMemory: 3270529352; totalMemory: 3300458496; maxMemory: 3817799680
[Wed Sep 28 23:24:37 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 13.25 minutes.
Runtime.totalMemory()=3300458496

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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/ZF3/out/qc/rep1/ZF3_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--------------------
3755 (process ID) old priority 0, new priority 10

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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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--------------------
9274 (process ID) old priority 0, new priority 10


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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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--------------------
9460 (process ID) old priority 0, new priority 10
Waiting for 23 seconds.

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

 

 
# 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/ZF3/out/align/rep1/ZF3_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/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr2/ZF3_allReps.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/pseudo_reps/rep1/pr1/ZF3_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--------------------
9459 (process ID) old priority 0, new priority 10

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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_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--------------------
5770 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_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/ZF3/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/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9764.1.q/Rtmpi7KdA6/ZF3_allReps.nodup.15M.tagAlign16f57674c0d6
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1964347 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.243184958979879 
Top 3 estimates for fragment length 115 
Window half size 400 
Phantom peak location 55 
Phantom peak Correlation 0.2332301 
Normalized Strand cross-correlation coefficient (NSC) 1.237994 
Relative Strand Cross correlation Coefficient (RSC) 1.270548 
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

 

 
# 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/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1 -speak=115 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_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/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

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

   
--------------------Stdout--------------------
9636 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 115 
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/ZF3/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/peak/spp/rep1/ZF3_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/ZF3/out/align/rep1/ZF3_allReps.nodup.tagAlign.gz 
opened /tmp/9765.1.q/RtmpnsrK6a/ZF3_allReps.nodup.tagAlign25e66755734a
done. read 30955688 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9765.1.q/RtmpnsrK6a/mousePrimaryBCellInput.nodup.tagAlign25e671d1360f
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.3217969 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.397981758925469 
Top 3 estimates for fragment length 115 
Window half size 400 
Phantom peak location 55 
Phantom peak Correlation 0.3818494 
Normalized Strand cross-correlation coefficient (NSC) 1.236748 
Relative Strand Cross correlation Coefficient (RSC) 1.268638 
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= 0.6066638  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 1.648359  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000056 
Detected 1225776 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 34 warnings (use warnings() to see them)

 

 
# SYS command. line 207

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

# SYS command. line 209

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/ZF3_IDR_final.qc

# SYS command. line 210

 echo -e "0\t""0\tN/A\tN/A\tNaN\tNaN\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/ZF3_IDR_final.qc

# SYS command. line 212

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

   
--------------------Stdout--------------------
37316 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

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

 

 
# SYS command. line 98

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

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/report/ZF3_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/report/ZF3_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/report/ZF3_workflow.svg" # to suppress dot font error (exit code=1)
 

   
--------------------Stdout--------------------
37422 (process ID) old priority 0, new priority 10

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

 

 
# SYS command. line 325

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

# SYS command. line 326

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF3/out/qc/rep1/ZF3_allReps.nodup.15M.cc.plot.pdf
 

   
--------------------Stdout--------------------
37460 (process ID) old priority 0, new priority 10

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