chipseq.bds.20160929_154340_049/task.callpeak_spp.spp_rep1.line_54.id_25
chipseq.bds.20160929_154340_049/task.callpeak_idr.idr_final_qc.line_205.id_26
chipseq.bds.20160929_154340_049/task.graphviz.report.line_97.id_27
chipseq.bds.20160929_154340_049/task.report.pdf2png.line_324.id_32
 

 chipseq.bds.20160929_154340_049_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20160929_154340_049_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20160929_154340_049_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 chipseq.bds.20160929_154340_049_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20160929_154340_049_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20160929_154340_049_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
chipseq.bds.20160929_154340_049_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
chipseq.bds.20160929_154340_049_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
chipseq.bds.20160929_154340_049_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 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_noBeads_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_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--------------------
28828 (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... 95.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.96 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.70 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... 88.34 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... 83.52 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... 95.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.70 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... 106.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.04 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.52 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.16 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.87 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.56 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.41 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.53 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.92 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.20 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.05 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.67 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.93 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.34 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.29 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.63 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.48 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.53 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.73 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 136362360 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_noBeads_allReps.fastq.gz
[main] Real time: 16281.437 sec; CPU: 55125.651 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 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai

# SYS command. line 115

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

   
--------------------Stdout--------------------
24129 (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] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.70 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... 56.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.11 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... 61.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.09 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... 54.69 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... 54.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.69 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.63 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.01 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.84 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.45 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.62 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.89 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.95 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.67 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.22 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.72 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.78 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.62 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.92 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz
[main] Real time: 6953.707 sec; CPU: 6953.504 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/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc

# SYS command. line 151

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

   
--------------------Stdout--------------------
37268 (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] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.59 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.62 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 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] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 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] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% 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] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% 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... 0.63 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% 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... 0.52 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.48 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% 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... 0.58 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.29 sec
[bwa_aln_core] print alignments... 0.10 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz
[main] Real time: 733.803 sec; CPU: 573.968 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/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
			    fi

# SYS command. line 116

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

   
--------------------Stdout--------------------
51718 (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/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 380

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

   
--------------------Stdout--------------------
9432 (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
[Thu Sep 29 18:09:01 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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
[Thu Sep 29 18:09:01 PDT 2016] Executing as imk1@nandi on Linux 3.16.0-67-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-29 18:09:02	MarkDuplicates	Start of doWork freeMemory: 255389384; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-29 18:09:02	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-29 18:09:02	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-29 18:09:20	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:   15s.  Last read position: chr1:169,651,309
INFO	2016-09-29 18:09:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:09:32	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:   11s.  Last read position: chr2:120,600,340
INFO	2016-09-29 18:09:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:09:38	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    5s.  Last read position: chr3:96,659,413
INFO	2016-09-29 18:09:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:09:48	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:   10s.  Last read position: chr4:108,195,091
INFO	2016-09-29 18:09:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:09:54	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    6s.  Last read position: chr5:103,594,339
INFO	2016-09-29 18:09:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:09:58	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    4s.  Last read position: chr6:98,592,333
INFO	2016-09-29 18:09:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:04	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    5s.  Last read position: chr7:114,109,505
INFO	2016-09-29 18:10:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:09	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    4s.  Last read position: chr8:121,515,352
INFO	2016-09-29 18:10:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:12	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    3s.  Last read position: chr10:14,536,964
INFO	2016-09-29 18:10:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:17	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    5s.  Last read position: chr11:32,924,585
INFO	2016-09-29 18:10:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:21	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr12:41,050,039
INFO	2016-09-29 18:10:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:24	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:    3s.  Last read position: chr13:80,878,598
INFO	2016-09-29 18:10:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:29	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    5s.  Last read position: chr15:12,027,335
INFO	2016-09-29 18:10:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:32	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    3s.  Last read position: chr16:56,024,589
INFO	2016-09-29 18:10:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:36	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    3s.  Last read position: chr18:10,030,498
INFO	2016-09-29 18:10:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:46	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    9s.  Last read position: chrX:36,565,109
INFO	2016-09-29 18:10:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 18:10:47	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-09-29 18:10:48	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2345227712; totalMemory: 2432368640; maxMemory: 3817799680
INFO	2016-09-29 18:10:48	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-29 18:10:49	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-29 18:10:49	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-29 18:10:55	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-29 18:10:56	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1922414832; totalMemory: 2898853888; maxMemory: 3817799680
INFO	2016-09-29 18:10:56	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-09-29 18:10:56	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-29 18:12:52	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:55s.  Time for last 10,000,000:  115s.  Last read position: chr11:32,924,585
INFO	2016-09-29 18:14:07	MarkDuplicates	Before output close freeMemory: 2896338792; totalMemory: 2924544000; maxMemory: 3817799680
INFO	2016-09-29 18:14:08	MarkDuplicates	After output close freeMemory: 2873203744; totalMemory: 2901409792; maxMemory: 3817799680
[Thu Sep 29 18:14:08 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 5.11 minutes.
Runtime.totalMemory()=2901409792

 

 
# SYS command. line 146

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

# SYS command. line 150

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

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc

# SYS command. line 169

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

   
--------------------Stdout--------------------
26278 (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/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz

# SYS command. line 511

 echo

# SYS command. line 513

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

   
--------------------Stdout--------------------
26374 (process ID) old priority 0, new priority 10

Waiting for 51 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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_noBeads_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_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--------------------
25249 (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... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.52 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.52 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.49 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.57 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.60 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.47 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.51 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.53 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.51 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.46 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.84 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.98 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.46 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.35 sec
[bwa_aln_core] refine gapped alignments... 6.17 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 65.32 sec
[bwa_aln_core] refine gapped alignments... 8.91 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.00 sec
[bwa_aln_core] refine gapped alignments... 10.35 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.13 sec
[bwa_aln_core] refine gapped alignments... 16.20 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 88.19 sec
[bwa_aln_core] refine gapped alignments... 8.72 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 91.62 sec
[bwa_aln_core] refine gapped alignments... 12.91 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.44 sec
[bwa_aln_core] refine gapped alignments... 6.96 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.50 sec
[bwa_aln_core] refine gapped alignments... 5.33 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.01 sec
[bwa_aln_core] refine gapped alignments... 8.82 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 92.97 sec
[bwa_aln_core] refine gapped alignments... 8.73 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.99 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.33 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.77 sec
[bwa_aln_core] refine gapped alignments... 8.65 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 66.46 sec
[bwa_aln_core] refine gapped alignments... 11.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.30 sec
[bwa_aln_core] refine gapped alignments... 16.78 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.82 sec
[bwa_aln_core] refine gapped alignments... 12.99 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.69 sec
[bwa_aln_core] refine gapped alignments... 10.99 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.28 sec
[bwa_aln_core] refine gapped alignments... 8.87 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.72 sec
[bwa_aln_core] refine gapped alignments... 4.54 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.30 sec
[bwa_aln_core] refine gapped alignments... 6.56 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.75 sec
[bwa_aln_core] refine gapped alignments... 7.37 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.55 sec
[bwa_aln_core] refine gapped alignments... 7.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.81 sec
[bwa_aln_core] refine gapped alignments... 3.99 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.23 sec
[bwa_aln_core] refine gapped alignments... 10.44 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.35 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.91 sec
[bwa_aln_core] refine gapped alignments... 11.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.94 sec
[bwa_aln_core] refine gapped alignments... 12.00 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.00 sec
[bwa_aln_core] refine gapped alignments... 10.70 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.36 sec
[bwa_aln_core] refine gapped alignments... 8.49 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.95 sec
[bwa_aln_core] refine gapped alignments... 7.83 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.03 sec
[bwa_aln_core] refine gapped alignments... 9.14 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.65 sec
[bwa_aln_core] refine gapped alignments... 9.93 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.14 sec
[bwa_aln_core] refine gapped alignments... 3.24 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.89 sec
[bwa_aln_core] refine gapped alignments... 7.02 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.81 sec
[bwa_aln_core] refine gapped alignments... 7.27 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.85 sec
[bwa_aln_core] refine gapped alignments... 3.36 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.88 sec
[bwa_aln_core] refine gapped alignments... 4.90 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.55 sec
[bwa_aln_core] refine gapped alignments... 5.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.11 sec
[bwa_aln_core] refine gapped alignments... 7.87 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.06 sec
[bwa_aln_core] refine gapped alignments... 7.01 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.85 sec
[bwa_aln_core] refine gapped alignments... 5.22 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.36 sec
[bwa_aln_core] refine gapped alignments... 8.07 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.12 sec
[bwa_aln_core] refine gapped alignments... 12.48 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.92 sec
[bwa_aln_core] refine gapped alignments... 11.14 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.80 sec
[bwa_aln_core] refine gapped alignments... 9.10 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.66 sec
[bwa_aln_core] refine gapped alignments... 7.17 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.28 sec
[bwa_aln_core] refine gapped alignments... 7.73 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.48 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.20 sec
[bwa_aln_core] refine gapped alignments... 9.71 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.78 sec
[bwa_aln_core] refine gapped alignments... 3.62 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.03 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.85 sec
[bwa_aln_core] refine gapped alignments... 10.38 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.32 sec
[bwa_aln_core] refine gapped alignments... 7.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.20 sec
[bwa_aln_core] refine gapped alignments... 4.51 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.9% 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... 0.71 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.92 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.13 sec
[bwa_aln_core] refine gapped alignments... 4.02 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.32 sec
[bwa_aln_core] refine gapped alignments... 6.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.39 sec
[bwa_aln_core] refine gapped alignments... 8.46 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.8% 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... 0.61 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.10 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.10 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.66 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.07 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.52 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.09 sec
[bwa_aln_core] refine gapped alignments... 8.93 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.78 sec
[bwa_aln_core] refine gapped alignments... 8.28 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.52 sec
[bwa_aln_core] refine gapped alignments... 12.46 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.18 sec
[bwa_aln_core] refine gapped alignments... 11.32 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.06 sec
[bwa_aln_core] refine gapped alignments... 11.95 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.78 sec
[bwa_aln_core] refine gapped alignments... 11.53 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.75 sec
[bwa_aln_core] refine gapped alignments... 11.54 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.45 sec
[bwa_aln_core] refine gapped alignments... 10.65 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.93 sec
[bwa_aln_core] refine gapped alignments... 10.98 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.44 sec
[bwa_aln_core] refine gapped alignments... 11.32 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 68.57 sec
[bwa_aln_core] refine gapped alignments... 11.49 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.24 sec
[bwa_aln_core] refine gapped alignments... 10.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.93 sec
[bwa_aln_core] refine gapped alignments... 10.78 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 68.53 sec
[bwa_aln_core] refine gapped alignments... 10.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.48 sec
[bwa_aln_core] refine gapped alignments... 10.92 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.59 sec
[bwa_aln_core] refine gapped alignments... 12.66 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.01 sec
[bwa_aln_core] refine gapped alignments... 12.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.55 sec
[bwa_aln_core] refine gapped alignments... 11.60 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.28 sec
[bwa_aln_core] refine gapped alignments... 11.03 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.95 sec
[bwa_aln_core] refine gapped alignments... 11.69 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.41 sec
[bwa_aln_core] refine gapped alignments... 11.71 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.69 sec
[bwa_aln_core] refine gapped alignments... 11.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.51 sec
[bwa_aln_core] refine gapped alignments... 11.83 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 72.25 sec
[bwa_aln_core] refine gapped alignments... 12.78 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.95 sec
[bwa_aln_core] refine gapped alignments... 10.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.39 sec
[bwa_aln_core] refine gapped alignments... 10.17 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.73 sec
[bwa_aln_core] refine gapped alignments... 9.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.77 sec
[bwa_aln_core] refine gapped alignments... 12.36 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.98 sec
[bwa_aln_core] refine gapped alignments... 12.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.44 sec
[bwa_aln_core] refine gapped alignments... 10.36 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.67 sec
[bwa_aln_core] refine gapped alignments... 9.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.76 sec
[bwa_aln_core] refine gapped alignments... 9.03 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.47 sec
[bwa_aln_core] refine gapped alignments... 9.12 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.21 sec
[bwa_aln_core] refine gapped alignments... 9.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.92 sec
[bwa_aln_core] refine gapped alignments... 9.88 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.02 sec
[bwa_aln_core] refine gapped alignments... 10.05 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.01 sec
[bwa_aln_core] refine gapped alignments... 9.73 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.14 sec
[bwa_aln_core] refine gapped alignments... 9.87 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.69 sec
[bwa_aln_core] refine gapped alignments... 10.69 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.55 sec
[bwa_aln_core] refine gapped alignments... 10.63 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.09 sec
[bwa_aln_core] refine gapped alignments... 9.58 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.81 sec
[bwa_aln_core] refine gapped alignments... 10.18 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.47 sec
[bwa_aln_core] refine gapped alignments... 10.69 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.81 sec
[bwa_aln_core] refine gapped alignments... 10.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.23 sec
[bwa_aln_core] refine gapped alignments... 10.10 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.31 sec
[bwa_aln_core] refine gapped alignments... 9.76 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.55 sec
[bwa_aln_core] refine gapped alignments... 9.82 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.65 sec
[bwa_aln_core] refine gapped alignments... 10.62 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 66.09 sec
[bwa_aln_core] refine gapped alignments... 9.77 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.35 sec
[bwa_aln_core] refine gapped alignments... 9.67 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.07 sec
[bwa_aln_core] refine gapped alignments... 10.27 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.42 sec
[bwa_aln_core] refine gapped alignments... 10.35 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.83 sec
[bwa_aln_core] refine gapped alignments... 10.03 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.75 sec
[bwa_aln_core] refine gapped alignments... 10.18 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.34 sec
[bwa_aln_core] refine gapped alignments... 11.65 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.61 sec
[bwa_aln_core] refine gapped alignments... 12.10 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.03 sec
[bwa_aln_core] refine gapped alignments... 12.14 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.71 sec
[bwa_aln_core] refine gapped alignments... 12.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.06 sec
[bwa_aln_core] refine gapped alignments... 12.07 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.32 sec
[bwa_aln_core] refine gapped alignments... 11.91 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.20 sec
[bwa_aln_core] refine gapped alignments... 11.81 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.46 sec
[bwa_aln_core] refine gapped alignments... 12.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.91 sec
[bwa_aln_core] refine gapped alignments... 12.90 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.92 sec
[bwa_aln_core] refine gapped alignments... 12.49 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.70 sec
[bwa_aln_core] refine gapped alignments... 12.57 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.24 sec
[bwa_aln_core] refine gapped alignments... 12.57 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.47 sec
[bwa_aln_core] refine gapped alignments... 12.75 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.78 sec
[bwa_aln_core] refine gapped alignments... 11.98 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.97 sec
[bwa_aln_core] refine gapped alignments... 12.09 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.02 sec
[bwa_aln_core] refine gapped alignments... 11.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.26 sec
[bwa_aln_core] refine gapped alignments... 11.80 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.69 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.66 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.49 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.71 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.97 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.70 sec
[bwa_aln_core] refine gapped alignments... 6.47 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.08 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.38 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.18 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.24 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.63 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.15 sec
[bwa_aln_core] 136362360 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/wt_noBeads_allReps.fastq.gz
[main] Real time: 12570.983 sec; CPU: 12031.356 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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_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--------------------
27729 (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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_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--------------------
6250 (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
[Fri Sep 30 00:09:47 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_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
[Fri Sep 30 00:09:47 PDT 2016] Executing as imk1@nandi on Linux 3.16.0-67-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-30 00:09:48	MarkDuplicates	Start of doWork freeMemory: 255389608; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-30 00:09:48	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-30 00:09:48	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-30 00:09:50	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836494.7652567'.  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	2016-09-30 00:10:01	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:   11s.  Last read position: chr1:36,279,395
INFO	2016-09-30 00:10:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:11	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    9s.  Last read position: chr1:63,301,449
INFO	2016-09-30 00:10:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:17	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    6s.  Last read position: chr1:90,150,879
INFO	2016-09-30 00:10:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:24	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    6s.  Last read position: chr1:123,216,498
INFO	2016-09-30 00:10:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:29	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    5s.  Last read position: chr1:148,739,798
INFO	2016-09-30 00:10:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:35	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    5s.  Last read position: chr1:172,357,716
INFO	2016-09-30 00:10:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:38	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr2:4,822,032
INFO	2016-09-30 00:10:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:42	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    4s.  Last read position: chr2:29,759,952
INFO	2016-09-30 00:10:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:44	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    1s.  Last read position: chr2:52,756,800
INFO	2016-09-30 00:10:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:47	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    2s.  Last read position: chr2:79,649,841
INFO	2016-09-30 00:10:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:52	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    5s.  Last read position: chr2:106,227,361
INFO	2016-09-30 00:10:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:54	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    1s.  Last read position: chr2:131,210,265
INFO	2016-09-30 00:10:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:10:57	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chr2:157,340,652
INFO	2016-09-30 00:10:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:03	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    6s.  Last read position: chr2:181,072,438
INFO	2016-09-30 00:11:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:05	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    1s.  Last read position: chr3:36,062,887
INFO	2016-09-30 00:11:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:14	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    9s.  Last read position: chr3:66,399,091
INFO	2016-09-30 00:11:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:16	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    1s.  Last read position: chr3:92,364,590
INFO	2016-09-30 00:11:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:18	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    1s.  Last read position: chr3:117,626,995
INFO	2016-09-30 00:11:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:21	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    2s.  Last read position: chr3:145,584,004
INFO	2016-09-30 00:11:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:23	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    1s.  Last read position: chr4:20,039,995
INFO	2016-09-30 00:11:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:24	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:34s.  Time for last 1,000,000:    1s.  Last read position: chr4:48,737,956
INFO	2016-09-30 00:11:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:28	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:37s.  Time for last 1,000,000:    3s.  Last read position: chr4:82,346,660
INFO	2016-09-30 00:11:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:30	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    1s.  Last read position: chr4:110,587,434
INFO	2016-09-30 00:11:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:31	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    1s.  Last read position: chr4:133,449,968
INFO	2016-09-30 00:11:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:34	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    3s.  Last read position: chr4:153,634,268
INFO	2016-09-30 00:11:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:37	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    2s.  Last read position: chr5:30,687,251
INFO	2016-09-30 00:11:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:43	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    5s.  Last read position: chr5:57,961,107
INFO	2016-09-30 00:11:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:44	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    1s.  Last read position: chr5:87,676,622
INFO	2016-09-30 00:11:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:47	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    2s.  Last read position: chr5:114,824,025
INFO	2016-09-30 00:11:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:11:52	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    4s.  Last read position: chr5:136,051,737
INFO	2016-09-30 00:11:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:00	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    8s.  Last read position: chr6:10,660,063
INFO	2016-09-30 00:12:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:03	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    2s.  Last read position: chr6:39,260,677
INFO	2016-09-30 00:12:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:06	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    3s.  Last read position: chr6:68,201,195
INFO	2016-09-30 00:12:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:08	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    1s.  Last read position: chr6:95,098,981
INFO	2016-09-30 00:12:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:10	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    1s.  Last read position: chr6:121,377,806
INFO	2016-09-30 00:12:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:12	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    1s.  Last read position: chr6:148,013,042
INFO	2016-09-30 00:12:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:14	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    1s.  Last read position: chr7:35,198,606
INFO	2016-09-30 00:12:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:17	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    3s.  Last read position: chr7:66,618,306
INFO	2016-09-30 00:12:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:20	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    2s.  Last read position: chr7:93,743,402
INFO	2016-09-30 00:12:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:23	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    2s.  Last read position: chr7:118,226,045
INFO	2016-09-30 00:12:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:26	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:    3s.  Last read position: chr7:141,489,355
INFO	2016-09-30 00:12:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:31	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    5s.  Last read position: chr8:27,269,850
INFO	2016-09-30 00:12:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:33	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    1s.  Last read position: chr8:59,312,679
INFO	2016-09-30 00:12:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:36	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    2s.  Last read position: chr8:85,194,151
INFO	2016-09-30 00:12:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:39	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    3s.  Last read position: chr8:111,192,992
INFO	2016-09-30 00:12:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:48	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    9s.  Last read position: chr9:8,599,596
INFO	2016-09-30 00:12:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:50	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    1s.  Last read position: chr9:38,229,651
INFO	2016-09-30 00:12:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:53	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    2s.  Last read position: chr9:60,810,028
INFO	2016-09-30 00:12:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:57	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    3s.  Last read position: chr9:83,240,330
INFO	2016-09-30 00:12:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:12:59	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:08s.  Time for last 1,000,000:    1s.  Last read position: chr9:109,897,553
INFO	2016-09-30 00:12:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:01	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    2s.  Last read position: chr10:13,356,892
INFO	2016-09-30 00:13:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:03	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    2s.  Last read position: chr10:41,618,282
INFO	2016-09-30 00:13:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:05	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    1s.  Last read position: chr10:67,944,230
INFO	2016-09-30 00:13:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:08	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    3s.  Last read position: chr10:89,942,778
INFO	2016-09-30 00:13:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:10	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    1s.  Last read position: chr10:117,807,817
INFO	2016-09-30 00:13:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:13	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    2s.  Last read position: chr11:15,048,459
INFO	2016-09-30 00:13:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:15	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    2s.  Last read position: chr11:43,710,648
INFO	2016-09-30 00:13:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:18	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    2s.  Last read position: chr11:65,697,242
INFO	2016-09-30 00:13:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:21	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    2s.  Last read position: chr11:84,339,676
INFO	2016-09-30 00:13:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:27	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    5s.  Last read position: chr11:103,106,167
INFO	2016-09-30 00:13:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:35	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    8s.  Last read position: chr11:121,354,210
INFO	2016-09-30 00:13:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:37	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    1s.  Last read position: chr12:35,699,235
INFO	2016-09-30 00:13:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:41	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chr12:67,942,869
INFO	2016-09-30 00:13:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:44	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    2s.  Last read position: chr12:91,803,260
INFO	2016-09-30 00:13:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:47	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    2s.  Last read position: chr12:117,606,762
INFO	2016-09-30 00:13:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:50	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    2s.  Last read position: chr13:30,945,592
INFO	2016-09-30 00:13:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:54	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    4s.  Last read position: chr13:54,621,649
INFO	2016-09-30 00:13:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:56	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    1s.  Last read position: chr13:85,853,528
INFO	2016-09-30 00:13:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:58	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    1s.  Last read position: chr13:112,659,307
INFO	2016-09-30 00:13:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:13:59	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    1s.  Last read position: chr14:29,370,882
INFO	2016-09-30 00:13:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:01	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    1s.  Last read position: chr14:59,024,293
INFO	2016-09-30 00:14:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:03	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    1s.  Last read position: chr14:83,922,851
INFO	2016-09-30 00:14:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:05	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    1s.  Last read position: chr14:116,321,470
INFO	2016-09-30 00:14:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:08	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:04:18s.  Time for last 1,000,000:    3s.  Last read position: chr15:25,414,667
INFO	2016-09-30 00:14:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:10	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    1s.  Last read position: chr15:56,310,326
INFO	2016-09-30 00:14:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:19	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    8s.  Last read position: chr15:79,685,177
INFO	2016-09-30 00:14:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:21	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    2s.  Last read position: chr15:100,680,699
INFO	2016-09-30 00:14:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:24	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    2s.  Last read position: chr16:23,303,759
INFO	2016-09-30 00:14:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:27	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    2s.  Last read position: chr16:48,438,221
INFO	2016-09-30 00:14:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:29	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    2s.  Last read position: chr16:79,180,060
INFO	2016-09-30 00:14:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:32	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    2s.  Last read position: chr17:11,195,984
INFO	2016-09-30 00:14:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:36	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    4s.  Last read position: chr17:34,094,359
INFO	2016-09-30 00:14:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:38	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    1s.  Last read position: chr17:56,929,327
INFO	2016-09-30 00:14:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:40	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    2s.  Last read position: chr17:84,632,532
INFO	2016-09-30 00:14:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:42	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    2s.  Last read position: chr18:23,647,144
INFO	2016-09-30 00:14:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:44	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    2s.  Last read position: chr18:50,932,610
INFO	2016-09-30 00:14:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:47	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:04:56s.  Time for last 1,000,000:    2s.  Last read position: chr18:76,378,866
INFO	2016-09-30 00:14:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:50	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:    3s.  Last read position: chr19:14,082,625
INFO	2016-09-30 00:14:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:52	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    1s.  Last read position: chr19:40,360,381
INFO	2016-09-30 00:14:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:14:55	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    2s.  Last read position: chrX:8,186,439
INFO	2016-09-30 00:14:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:15:04	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    9s.  Last read position: chrX:73,798,337
INFO	2016-09-30 00:15:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:15:06	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    1s.  Last read position: chrX:130,151,931
INFO	2016-09-30 00:15:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:15:09	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    2s.  Last read position: chrM:14,780
INFO	2016-09-30 00:15:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-30 00:15:09	MarkDuplicates	Read 93089603 records. 0 pairs never matched.
INFO	2016-09-30 00:15:10	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2589743608; totalMemory: 2677080064; maxMemory: 3817799680
INFO	2016-09-30 00:15:10	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-30 00:15:10	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-30 00:15:10	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-30 00:15:30	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-30 00:15:32	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2154031600; totalMemory: 3134259200; maxMemory: 3817799680
INFO	2016-09-30 00:15:32	MarkDuplicates	Marking 25247989 records as duplicates.
INFO	2016-09-30 00:15:32	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-30 00:17:01	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 10,000,000:   89s.  Last read position: chr2:79,649,841
INFO	2016-09-30 00:18:31	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:59s.  Time for last 10,000,000:   89s.  Last read position: chr4:20,039,995
INFO	2016-09-30 00:20:01	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:29s.  Time for last 10,000,000:   90s.  Last read position: chr5:136,051,737
INFO	2016-09-30 00:21:32	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:00s.  Time for last 10,000,000:   91s.  Last read position: chr7:118,226,045
INFO	2016-09-30 00:23:03	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:31s.  Time for last 10,000,000:   91s.  Last read position: chr9:109,897,553
INFO	2016-09-30 00:24:34	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:09:02s.  Time for last 10,000,000:   91s.  Last read position: chr11:103,106,167
INFO	2016-09-30 00:26:04	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:10:32s.  Time for last 10,000,000:   89s.  Last read position: chr14:29,370,882
INFO	2016-09-30 00:27:33	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:12:01s.  Time for last 10,000,000:   89s.  Last read position: chr16:79,180,060
INFO	2016-09-30 00:29:01	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:13:29s.  Time for last 10,000,000:   88s.  Last read position: chrX:8,186,439
INFO	2016-09-30 00:29:29	MarkDuplicates	Before output close freeMemory: 3201399952; totalMemory: 3231186944; maxMemory: 3817799680
INFO	2016-09-30 00:29:30	MarkDuplicates	After output close freeMemory: 3201401736; totalMemory: 3231186944; maxMemory: 3817799680
[Fri Sep 30 00:29:30 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 19.71 minutes.
Runtime.totalMemory()=3231186944

 

 
# SYS command. line 146

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

# SYS command. line 150

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

# SYS command. line 153

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

# SYS command. line 155

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

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_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--------------------
22375 (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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_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--------------------
23828 (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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_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--------------------
24088 (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 249

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

# SYS command. line 252

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

# SYS command. line 253

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

# SYS command. line 257

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

# SYS command. line 260

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

# SYS command. line 261

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

# SYS command. line 262

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

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/pseudo_reps/rep1/pr1/wt_noBeads_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--------------------
24087 (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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.qc 

# SYS command. line 219

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

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_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--------------------
2396 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 4 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9919.1.q/RtmpjE6Zb4/wt_noBeads_allReps.nodup.15M.tagAligna721ab53010
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1899526 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.216448846588994 
Top 3 estimates for fragment length 110 
Window half size 290 
Phantom peak location 55 
Phantom peak Correlation 0.2101819 
Normalized Strand cross-correlation coefficient (NSC) 1.139489 
Relative Strand Cross correlation Coefficient (RSC) 1.309797 
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/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1 -speak=110 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.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--------------------
25155 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 110 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/peak/spp/rep1/wt_noBeads_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/rep1/wt_noBeads_allReps.nodup.tagAlign.gz 
opened /tmp/9920.1.q/RtmpgOWPzD/wt_noBeads_allReps.nodup.tagAlign62857718c50c
done. read 67841614 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz 
opened /tmp/9920.1.q/RtmpgOWPzD/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign62851ea88de0
done. read 3384182 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.4880046 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.555548338772688 
Top 3 estimates for fragment length 110 
Window half size 285 
Phantom peak location 55 
Phantom peak Correlation 0.5397497 
Normalized Strand cross-correlation coefficient (NSC) 1.138408 
Relative Strand Cross correlation Coefficient (RSC) 1.305317 
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= 0.05147466  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 19.42704  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000023 
Detected 3267925 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 36 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/WT_NOBEADS/out/qc/WT_NOBEADS_IDR_final.qc

# SYS command. line 210

 echo -e "0\t""0\tN/A\tN/A\tNaN\tNaN\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/WT_NOBEADS_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--------------------
30024 (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/WT_NOBEADS/out/report/WT_NOBEADS_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/report/WT_NOBEADS_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/report/WT_NOBEADS_workflow.svg" # to suppress dot font error (exit code=1)
 

   
--------------------Stdout--------------------
6100 (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/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/WT_NOBEADS/out/qc/rep1/wt_noBeads_allReps.nodup.15M.cc.plot.pdf
 

   
--------------------Stdout--------------------
6140 (process ID) old priority 0, new priority 10

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