xcor rep1

 chipseq.bds.20161101_222022_418_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20161101_222022_418_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20161101_222022_418_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20161101_222022_418_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15
chipseq.bds.20161101_222022_418_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20161101_222022_418_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17
 

 chipseq.bds.20161101_222022_418_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20161101_222022_418_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 
# 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/SRR836456.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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--------------------
17643 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.67 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.32 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... 32.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.71 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.98 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.71 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.36 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
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[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.89 sec
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[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.29 sec
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[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.82 sec
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[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.97 sec
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[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
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[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
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[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
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[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.12 sec
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[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
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[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.28 sec
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[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.57 sec
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[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.69 sec
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] calculate SA coordinate... 29.48 sec
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[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.98 sec
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[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.18 sec
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
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[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.23 sec
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[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.16 sec
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[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.45 sec
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[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.12 sec
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[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.91 sec
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[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 204210176 sequences have been processed.
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[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.08 sec
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[bwa_aln_core] 205783040 sequences have been processed.
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 206569472 sequences have been processed.
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[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
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[bwa_read_seq] 0.8% bases are trimmed.
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[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
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[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
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[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
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[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.74 sec
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[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
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[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 209453056 sequences have been processed.
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[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 210239488 sequences have been processed.
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[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 210763776 sequences have been processed.
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[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 211550208 sequences have been processed.
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[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
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[bwa_aln_core] 212860928 sequences have been processed.
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[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 213385216 sequences have been processed.
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[bwa_aln_core] 214433792 sequences have been processed.
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[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 215482368 sequences have been processed.
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[bwa_aln_core] 215744512 sequences have been processed.
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[bwa_aln_core] 216006656 sequences have been processed.
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[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 216530944 sequences have been processed.
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[bwa_aln_core] 216793088 sequences have been processed.
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[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 247726080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 247988224 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 249298944 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 249823232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250347520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250609664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 250871808 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 251133952 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 8.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 251204134 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/SRR836456.fastq.gz
[main] Real time: 8718.623 sec; CPU: 29113.536 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/SRR836456/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--------------------
24964 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.16 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... 57.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.44 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... 55.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.95 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.70 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... 62.60 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.59 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... 59.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.18 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... 52.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.85 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.63 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.33 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... 52.16 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.51 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... 64.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.50 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... 62.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.83 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.02 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.21 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... 52.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.36 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.61 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.35 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.86 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.38 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... 54.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.11 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.89 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... 51.18 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.76 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... 50.24 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... 52.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.60 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.01 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... 57.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.81 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... 50.18 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... 47.30 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... 48.68 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... 47.63 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... 47.45 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.42 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... 48.71 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... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.32 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... 48.15 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... 48.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 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... 50.07 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... 53.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.10 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... 56.02 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... 60.20 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... 61.69 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.80 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... 50.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.80 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... 46.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.26 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... 46.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.30 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... 46.51 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... 47.00 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... 46.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.03 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... 47.08 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... 46.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.28 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... 47.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.29 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 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... 50.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.83 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: 6574.743 sec; CPU: 6577.960 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/SRR836456/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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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--------------------
28479 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.65 sec
[bwa_aln_core] refine gapped alignments... 5.48 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.33 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.99 sec
[bwa_aln_core] refine gapped alignments... 3.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.59 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.95 sec
[bwa_aln_core] refine gapped alignments... 3.92 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.46 sec
[bwa_aln_core] refine gapped alignments... 4.57 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.37 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.36 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.36 sec
[bwa_aln_core] refine gapped alignments... 4.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.06 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.39 sec
[bwa_aln_core] refine gapped alignments... 4.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.02 sec
[bwa_aln_core] refine gapped alignments... 18.90 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 115.85 sec
[bwa_aln_core] refine gapped alignments... 18.24 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 117.74 sec
[bwa_aln_core] refine gapped alignments... 19.89 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 114.05 sec
[bwa_aln_core] refine gapped alignments... 20.61 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 120.16 sec
[bwa_aln_core] refine gapped alignments... 21.67 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 114.96 sec
[bwa_aln_core] refine gapped alignments... 7.30 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.21 sec
[bwa_aln_core] refine gapped alignments... 3.72 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.25 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.61 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.31 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.88 sec
[bwa_aln_core] refine gapped alignments... 4.68 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.72 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 111.44 sec
[bwa_aln_core] refine gapped alignments... 19.65 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 112.89 sec
[bwa_aln_core] refine gapped alignments... 19.70 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 112.43 sec
[bwa_aln_core] refine gapped alignments... 18.90 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 110.15 sec
[bwa_aln_core] refine gapped alignments... 20.21 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.23 sec
[bwa_aln_core] refine gapped alignments... 5.02 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.87 sec
[bwa_aln_core] refine gapped alignments... 3.93 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.34 sec
[bwa_aln_core] refine gapped alignments... 4.18 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.60 sec
[bwa_aln_core] refine gapped alignments... 3.78 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.41 sec
[bwa_aln_core] refine gapped alignments... 4.32 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.77 sec
[bwa_aln_core] refine gapped alignments... 3.53 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.43 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.50 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.17 sec
[bwa_aln_core] refine gapped alignments... 3.68 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.88 sec
[bwa_aln_core] refine gapped alignments... 3.99 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.66 sec
[bwa_aln_core] refine gapped alignments... 5.07 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.65 sec
[bwa_aln_core] refine gapped alignments... 3.57 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.28 sec
[bwa_aln_core] refine gapped alignments... 3.57 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.02 sec
[bwa_aln_core] refine gapped alignments... 4.19 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.25 sec
[bwa_aln_core] refine gapped alignments... 4.46 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.79 sec
[bwa_aln_core] refine gapped alignments... 4.02 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.04 sec
[bwa_aln_core] refine gapped alignments... 3.98 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.82 sec
[bwa_aln_core] refine gapped alignments... 3.07 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.86 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.29 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.89 sec
[bwa_aln_core] refine gapped alignments... 4.09 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.64 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.74 sec
[bwa_aln_core] refine gapped alignments... 4.29 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.39 sec
[bwa_aln_core] refine gapped alignments... 3.89 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.47 sec
[bwa_aln_core] refine gapped alignments... 5.77 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.39 sec
[bwa_aln_core] refine gapped alignments... 3.67 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.53 sec
[bwa_aln_core] refine gapped alignments... 3.95 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.20 sec
[bwa_aln_core] refine gapped alignments... 3.75 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.09 sec
[bwa_aln_core] refine gapped alignments... 4.07 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.14 sec
[bwa_aln_core] refine gapped alignments... 3.89 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.05 sec
[bwa_aln_core] refine gapped alignments... 3.71 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.98 sec
[bwa_aln_core] refine gapped alignments... 3.73 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.47 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.47 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.68 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.70 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.64 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.37 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.65 sec
[bwa_aln_core] refine gapped alignments... 3.95 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.61 sec
[bwa_aln_core] refine gapped alignments... 3.85 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.12 sec
[bwa_aln_core] refine gapped alignments... 3.89 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.32 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.15 sec
[bwa_aln_core] refine gapped alignments... 4.03 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.48 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.07 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.67 sec
[bwa_aln_core] refine gapped alignments... 3.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.44 sec
[bwa_aln_core] refine gapped alignments... 3.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.64 sec
[bwa_aln_core] refine gapped alignments... 4.00 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.93 sec
[bwa_aln_core] refine gapped alignments... 4.03 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.01 sec
[bwa_aln_core] refine gapped alignments... 4.56 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.85 sec
[bwa_aln_core] refine gapped alignments... 4.08 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.33 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.73 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.80 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.56 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.65 sec
[bwa_aln_core] refine gapped alignments... 6.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.76 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.93 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.78 sec
[bwa_aln_core] refine gapped alignments... 4.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.79 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.45 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.46 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.54 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.92 sec
[bwa_aln_core] refine gapped alignments... 3.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.18 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.65 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.45 sec
[bwa_aln_core] refine gapped alignments... 1.56 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.95 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.96 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.18 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.48 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.61 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.77 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.97 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.48 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.84 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.87 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.87 sec
[bwa_aln_core] refine gapped alignments... 2.02 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.06 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.33 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.57 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.63 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.91 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.48 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.05 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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: 4596.957 sec; CPU: 4430.476 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/SRR836456/out/align/rep1/SRR836456.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836456.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.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--------------------
18370 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.81 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.79 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.84 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.56 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.28 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.75 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.60 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.77 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.60 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.69 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.89 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.46 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.78 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.59 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.47 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.08 sec
[bwa_aln_core] refine gapped alignments... 3.79 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.29 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.49 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 39845888 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... 0.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 40632320 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... 0.60 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.77 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.22 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.43 sec
[bwa_aln_core] refine gapped alignments... 1.97 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.52 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.52 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.41 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.75 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.76 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.76 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.16 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.46 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.67 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.91 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.93 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.37 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.72 sec
[bwa_aln_core] refine gapped alignments... 1.43 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.26 sec
[bwa_aln_core] refine gapped alignments... 7.26 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.60 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.73 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.32 sec
[bwa_aln_core] refine gapped alignments... 7.27 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.98 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.30 sec
[bwa_aln_core] refine gapped alignments... 5.83 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.99 sec
[bwa_aln_core] refine gapped alignments... 7.85 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.17 sec
[bwa_aln_core] refine gapped alignments... 6.70 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.90 sec
[bwa_aln_core] refine gapped alignments... 5.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.41 sec
[bwa_aln_core] refine gapped alignments... 2.58 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.69 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.75 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 1.40 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.33 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.26 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.73 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.46 sec
[bwa_aln_core] refine gapped alignments... 5.27 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.72 sec
[bwa_aln_core] refine gapped alignments... 10.32 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.09 sec
[bwa_aln_core] refine gapped alignments... 6.89 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.82 sec
[bwa_aln_core] refine gapped alignments... 1.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.14 sec
[bwa_aln_core] refine gapped alignments... 3.78 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.33 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.39 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.69 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.76 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.76 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.36 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.89 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.38 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.93 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.02 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.36 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.81 sec
[bwa_aln_core] refine gapped alignments... 0.72 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.16 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 81264640 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... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.8% 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... 0.78 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.8% 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... 0.81 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.76 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.88 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.22 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.84 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.75 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.78 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.79 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.10 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.75 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.79 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.77 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.76 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.76 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.76 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 0.7% 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... 0.80 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 0.7% 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... 0.76 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 0.8% 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... 0.77 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 123207680 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... 0.65 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.91 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.25 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.24 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.87 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.63 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.30 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.25 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.38 sec
[bwa_aln_core] refine gapped alignments... 10.91 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 73.19 sec
[bwa_aln_core] refine gapped alignments... 11.28 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.26 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.57 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.67 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.70 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.89 sec
[bwa_aln_core] refine gapped alignments... 1.41 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.18 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.91 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.00 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.43 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.46 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.38 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.23 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.46 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.75 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.83 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.27 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.17 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.70 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.97 sec
[bwa_aln_core] refine gapped alignments... 3.05 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.57 sec
[bwa_aln_core] refine gapped alignments... 10.85 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.34 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.57 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.18 sec
[bwa_aln_core] refine gapped alignments... 8.76 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.51 sec
[bwa_aln_core] refine gapped alignments... 4.65 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 59.62 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.09 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.74 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.76 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.81 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.81 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.29 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 164626432 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... 0.58 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 165412864 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... 0.56 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 165937152 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... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 0.7% 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... 0.76 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.20 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.76 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.84 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.72 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.88 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.51 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.61 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.51 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.84 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.24 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.54 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.99 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.45 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.21 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 196083712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.14 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.89 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
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[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
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[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
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[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.79 sec
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[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
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[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.39 sec
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[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.93 sec
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[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.22 sec
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[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 62.39 sec
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[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.99 sec
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[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.69 sec
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[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.19 sec
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[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.84 sec
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[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
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[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
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[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
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[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
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[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.62 sec
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[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.39 sec
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[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.10 sec
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[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 77.33 sec
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[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.84 sec
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[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.11 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
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[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.19 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
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[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.65 sec
[bwa_aln_core] refine gapped alignments... 3.89 sec
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[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.05 sec
[bwa_aln_core] refine gapped alignments... 6.38 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.81 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
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[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 3.57 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.95 sec
[bwa_aln_core] refine gapped alignments... 6.27 sec
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[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.75 sec
[bwa_aln_core] refine gapped alignments... 6.96 sec
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[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.43 sec
[bwa_aln_core] refine gapped alignments... 7.24 sec
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[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.40 sec
[bwa_aln_core] refine gapped alignments... 7.24 sec
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[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.72 sec
[bwa_aln_core] refine gapped alignments... 3.66 sec
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[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.68 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
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[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.93 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
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[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.70 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
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[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.10 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
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[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.81 sec
[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
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[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
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[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
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[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
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[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
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[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
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[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
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[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.62 sec
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[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.43 sec
[bwa_aln_core] refine gapped alignments... 10.34 sec
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[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.42 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
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[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.24 sec
[bwa_aln_core] refine gapped alignments... 8.48 sec
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[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.03 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
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[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.14 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
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[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.10 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
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[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
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[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
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[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
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[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
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[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
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[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
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[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
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[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
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[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
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[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
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[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
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[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
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[bwa_aln_core] 216793088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
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[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
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[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
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[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
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[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.93 sec
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[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
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[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.77 sec
[bwa_aln_core] refine gapped alignments... 5.82 sec
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[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.50 sec
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[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
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[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
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[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
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[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
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[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
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[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
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[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
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[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
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[bwa_aln_core] 221249536 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... 0.47 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.77 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.68 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.20 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 64.33 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.08 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 0.7% 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... 0.77 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.83 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 0.7% 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... 0.41 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 247726080 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 247988224 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... 0.48 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 249298944 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... 0.54 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 249823232 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... 0.50 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 250347520 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... 0.79 sec
[bwa_aln_core] 250609664 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 250871808 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... 0.55 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 251133952 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.64 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 251204134 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/SRR836456/out/align/rep1/SRR836456.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836456.fastq.gz
[main] Real time: 11826.913 sec; CPU: 10086.012 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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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--------------------
30808 (process ID) old priority 0, new priority 10

  

 
# 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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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--------------------
14414 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 03:07:54 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 02 03:07:54 PDT 2016] Executing as imk1@surya on Linux 4.4.0-31-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 03:07:55	MarkDuplicates	Start of doWork freeMemory: 254881776; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 03:07:55	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 03:07:55	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 03:08:01	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr1:169,651,309
INFO	2016-11-02 03:08:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:07	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    5s.  Last read position: chr2:120,600,340
INFO	2016-11-02 03:08:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:13	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    6s.  Last read position: chr3:96,659,413
INFO	2016-11-02 03:08:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:19	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    6s.  Last read position: chr4:108,195,091
INFO	2016-11-02 03:08:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:22	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    2s.  Last read position: chr5:103,594,339
INFO	2016-11-02 03:08:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:27	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    5s.  Last read position: chr6:98,592,333
INFO	2016-11-02 03:08:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:30	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    2s.  Last read position: chr7:114,109,505
INFO	2016-11-02 03:08:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:33	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    3s.  Last read position: chr8:121,515,352
INFO	2016-11-02 03:08:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:37	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    4s.  Last read position: chr10:14,536,964
INFO	2016-11-02 03:08:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:42	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    4s.  Last read position: chr11:32,924,585
INFO	2016-11-02 03:08:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:46	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    3s.  Last read position: chr12:41,050,039
INFO	2016-11-02 03:08:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:49	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    3s.  Last read position: chr13:80,878,598
INFO	2016-11-02 03:08:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:53	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    3s.  Last read position: chr15:12,027,335
INFO	2016-11-02 03:08:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:08:58	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    5s.  Last read position: chr16:56,024,589
INFO	2016-11-02 03:08:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:09:10	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:   12s.  Last read position: chr18:10,030,498
INFO	2016-11-02 03:09:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:09:13	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:18s.  Time for last 1,000,000:    3s.  Last read position: chrX:36,565,109
INFO	2016-11-02 03:09:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:09:16	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 03:09:16	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2566129384; totalMemory: 2652372992; maxMemory: 3817865216
INFO	2016-11-02 03:09:16	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 03:09:17	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 03:09:17	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 03:09:21	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 03:09:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1931323776; totalMemory: 2912944128; maxMemory: 3817865216
INFO	2016-11-02 03:09:22	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 03:09:22	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 03:10:37	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:14s.  Time for last 10,000,000:   74s.  Last read position: chr11:32,924,585
INFO	2016-11-02 03:11:28	MarkDuplicates	Before output close freeMemory: 2982042568; totalMemory: 3010985984; maxMemory: 3817865216
INFO	2016-11-02 03:11:28	MarkDuplicates	After output close freeMemory: 2962118568; totalMemory: 2991063040; maxMemory: 3817865216
[Wed Nov 02 03:11:28 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.57 minutes.
Runtime.totalMemory()=2991063040

 

 
# 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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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/SRR836456/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/SRR836456/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/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/SRR836456/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/SRR836456/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--------------------
26666 (process ID) old priority 0, new priority 10

  

 
# 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/SRR836456/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/SRR836456/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--------------------
27178 (process ID) old priority 0, new priority 10

Waiting for 52 seconds.

  

 
# 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/SRR836456/out/align/rep1/SRR836456.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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/SRR836456/out/align/rep1/SRR836456.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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--------------------
46471 (process ID) old priority 0, new priority 10

  

 
# 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/SRR836456/out/align/rep1/SRR836456.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.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--------------------
12063 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 08:51:40 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 02 08:51:40 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 08:51:40	MarkDuplicates	Start of doWork freeMemory: 254882416; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 08:51:40	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 08:51:40	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 08:51:40	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836456.182761301'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2016-11-02 08:51:43	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:25,193,829
INFO	2016-11-02 08:51:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:51:46	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr1:39,594,799
INFO	2016-11-02 08:51:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:51:49	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    2s.  Last read position: chr1:57,662,301
INFO	2016-11-02 08:51:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:51:52	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    2s.  Last read position: chr1:73,940,685
INFO	2016-11-02 08:51:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:51:55	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    3s.  Last read position: chr1:86,215,896
INFO	2016-11-02 08:51:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:51:59	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    4s.  Last read position: chr1:92,912,141
INFO	2016-11-02 08:51:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:03	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    3s.  Last read position: chr1:119,532,553
INFO	2016-11-02 08:52:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:09	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    6s.  Last read position: chr1:132,157,685
INFO	2016-11-02 08:52:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:17	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    7s.  Last read position: chr1:139,436,249
INFO	2016-11-02 08:52:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:21	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    4s.  Last read position: chr1:156,954,449
INFO	2016-11-02 08:52:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:25	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr1:169,575,806
INFO	2016-11-02 08:52:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:29	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    4s.  Last read position: chr1:180,114,249
INFO	2016-11-02 08:52:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:34	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    4s.  Last read position: chr1:189,483,086
INFO	2016-11-02 08:52:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:52:37	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr2:6,319,701
INFO	2016-11-02 08:52:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:00	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:   22s.  Last read position: chr2:23,068,148
INFO	2016-11-02 08:53:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:03	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:    2s.  Last read position: chr2:28,607,189
INFO	2016-11-02 08:53:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:05	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    2s.  Last read position: chr2:32,750,831
INFO	2016-11-02 08:53:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:09	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:28s.  Time for last 1,000,000:    3s.  Last read position: chr2:44,369,906
INFO	2016-11-02 08:53:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:12	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    2s.  Last read position: chr2:62,758,116
INFO	2016-11-02 08:53:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:16	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:    3s.  Last read position: chr2:75,832,400
INFO	2016-11-02 08:53:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:20	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    4s.  Last read position: chr2:92,485,081
INFO	2016-11-02 08:53:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:25	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    4s.  Last read position: chr2:104,489,701
INFO	2016-11-02 08:53:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:28	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    2s.  Last read position: chr2:119,762,488
INFO	2016-11-02 08:53:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:30	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    2s.  Last read position: chr2:128,493,828
INFO	2016-11-02 08:53:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:34	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    3s.  Last read position: chr2:141,522,360
INFO	2016-11-02 08:53:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:37	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:56s.  Time for last 1,000,000:    3s.  Last read position: chr2:152,916,650
INFO	2016-11-02 08:53:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    3s.  Last read position: chr2:158,836,544
INFO	2016-11-02 08:53:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:44	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    3s.  Last read position: chr2:166,646,963
INFO	2016-11-02 08:53:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:47	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    3s.  Last read position: chr2:172,976,151
INFO	2016-11-02 08:53:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:56	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    8s.  Last read position: chr3:3,031,693
INFO	2016-11-02 08:53:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:53:59	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    3s.  Last read position: chr3:28,746,211
INFO	2016-11-02 08:53:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:03	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    3s.  Last read position: chr3:50,743,328
INFO	2016-11-02 08:54:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:05	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    2s.  Last read position: chr3:65,441,834
INFO	2016-11-02 08:54:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:08	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    2s.  Last read position: chr3:84,781,878
INFO	2016-11-02 08:54:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:11	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    2s.  Last read position: chr3:90,459,881
INFO	2016-11-02 08:54:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:16	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    5s.  Last read position: chr3:100,492,180
INFO	2016-11-02 08:54:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:19	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    2s.  Last read position: chr3:109,550,873
INFO	2016-11-02 08:54:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:22	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr3:129,488,967
INFO	2016-11-02 08:54:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:24	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    2s.  Last read position: chr3:144,198,014
INFO	2016-11-02 08:54:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:27	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    2s.  Last read position: chr4:5,034,196
INFO	2016-11-02 08:54:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:30	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    2s.  Last read position: chr4:29,588,342
INFO	2016-11-02 08:54:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:33	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    3s.  Last read position: chr4:44,462,046
INFO	2016-11-02 08:54:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:39	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    5s.  Last read position: chr4:55,653,117
INFO	2016-11-02 08:54:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:43	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    4s.  Last read position: chr4:72,522,796
INFO	2016-11-02 08:54:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:53	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:   10s.  Last read position: chr4:97,037,764
INFO	2016-11-02 08:54:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:54:57	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    3s.  Last read position: chr4:108,643,599
INFO	2016-11-02 08:54:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:01	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    3s.  Last read position: chr4:119,632,318
INFO	2016-11-02 08:55:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:04	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    3s.  Last read position: chr4:127,694,660
INFO	2016-11-02 08:55:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:08	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:    3s.  Last read position: chr4:133,219,476
INFO	2016-11-02 08:55:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:11	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    3s.  Last read position: chr4:136,897,865
INFO	2016-11-02 08:55:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:16	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    4s.  Last read position: chr4:141,690,416
INFO	2016-11-02 08:55:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:18	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    2s.  Last read position: chr4:150,626,614
INFO	2016-11-02 08:55:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:21	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    2s.  Last read position: chr5:3,543,821
INFO	2016-11-02 08:55:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:23	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    2s.  Last read position: chr5:24,975,118
INFO	2016-11-02 08:55:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:26	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:03:45s.  Time for last 1,000,000:    2s.  Last read position: chr5:34,312,677
INFO	2016-11-02 08:55:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:29	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    3s.  Last read position: chr5:47,000,336
INFO	2016-11-02 08:55:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:32	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chr5:66,693,503
INFO	2016-11-02 08:55:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:35	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    2s.  Last read position: chr5:88,347,385
INFO	2016-11-02 08:55:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:45	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:   10s.  Last read position: chr5:103,630,298
INFO	2016-11-02 08:55:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:48	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    3s.  Last read position: chr5:112,890,689
INFO	2016-11-02 08:55:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:51	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    3s.  Last read position: chr5:118,548,885
INFO	2016-11-02 08:55:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:55	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    3s.  Last read position: chr5:123,444,324
INFO	2016-11-02 08:55:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:55:58	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    3s.  Last read position: chr5:131,426,131
INFO	2016-11-02 08:55:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:01	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:    2s.  Last read position: chr5:137,962,089
INFO	2016-11-02 08:56:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:04	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    3s.  Last read position: chr5:144,223,037
INFO	2016-11-02 08:56:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:08	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    3s.  Last read position: chr6:3,860,565
INFO	2016-11-02 08:56:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:14	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    5s.  Last read position: chr6:29,103,364
INFO	2016-11-02 08:56:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:17	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    3s.  Last read position: chr6:39,359,324
INFO	2016-11-02 08:56:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:20	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    2s.  Last read position: chr6:52,506,603
INFO	2016-11-02 08:56:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:23	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    3s.  Last read position: chr6:71,440,911
INFO	2016-11-02 08:56:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:27	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    3s.  Last read position: chr6:85,537,534
INFO	2016-11-02 08:56:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:29	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    2s.  Last read position: chr6:91,878,589
INFO	2016-11-02 08:56:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:32	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    2s.  Last read position: chr6:108,427,399
INFO	2016-11-02 08:56:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:40	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:04:59s.  Time for last 1,000,000:    7s.  Last read position: chr6:118,381,073
INFO	2016-11-02 08:56:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:43	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    2s.  Last read position: chr6:126,564,057
INFO	2016-11-02 08:56:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:46	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    3s.  Last read position: chr6:137,911,586
INFO	2016-11-02 08:56:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:48	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    2s.  Last read position: chr7:4,202,940
INFO	2016-11-02 08:56:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:51	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    2s.  Last read position: chr7:19,329,065
INFO	2016-11-02 08:56:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:53	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    2s.  Last read position: chr7:28,320,408
INFO	2016-11-02 08:56:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:56	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    2s.  Last read position: chr7:36,473,353
INFO	2016-11-02 08:56:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:56:58	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    2s.  Last read position: chr7:45,941,852
INFO	2016-11-02 08:56:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:01	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    2s.  Last read position: chr7:65,519,995
INFO	2016-11-02 08:57:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:03	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    2s.  Last read position: chr7:79,273,356
INFO	2016-11-02 08:57:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:06	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:05:25s.  Time for last 1,000,000:    2s.  Last read position: chr7:90,442,993
INFO	2016-11-02 08:57:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:10	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    4s.  Last read position: chr7:101,368,043
INFO	2016-11-02 08:57:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:13	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    2s.  Last read position: chr7:113,184,633
INFO	2016-11-02 08:57:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:16	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    2s.  Last read position: chr7:122,730,322
INFO	2016-11-02 08:57:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:20	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    4s.  Last read position: chr7:128,752,823
INFO	2016-11-02 08:57:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:27	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:05:46s.  Time for last 1,000,000:    7s.  Last read position: chr7:139,418,128
INFO	2016-11-02 08:57:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:30	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    3s.  Last read position: chr8:3,460,329
INFO	2016-11-02 08:57:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:33	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:05:52s.  Time for last 1,000,000:    3s.  Last read position: chr8:16,483,788
INFO	2016-11-02 08:57:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:37	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    4s.  Last read position: chr8:32,713,744
INFO	2016-11-02 08:57:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:40	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:05:59s.  Time for last 1,000,000:    3s.  Last read position: chr8:47,879,646
INFO	2016-11-02 08:57:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:44	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:06:03s.  Time for last 1,000,000:    3s.  Last read position: chr8:70,235,189
INFO	2016-11-02 08:57:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:47	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    3s.  Last read position: chr8:79,273,567
INFO	2016-11-02 08:57:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:53	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:06:12s.  Time for last 1,000,000:    5s.  Last read position: chr8:88,198,977
INFO	2016-11-02 08:57:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:55	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    2s.  Last read position: chr8:103,144,713
INFO	2016-11-02 08:57:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:57:58	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    2s.  Last read position: chr8:111,029,396
INFO	2016-11-02 08:57:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:00	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    2s.  Last read position: chr8:120,072,449
INFO	2016-11-02 08:58:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:03	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    2s.  Last read position: chr8:124,239,255
INFO	2016-11-02 08:58:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:06	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    2s.  Last read position: chr9:13,627,261
INFO	2016-11-02 08:58:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:08	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    2s.  Last read position: chr9:24,725,281
INFO	2016-11-02 08:58:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:14	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    6s.  Last read position: chr9:40,452,537
INFO	2016-11-02 08:58:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:17	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    2s.  Last read position: chr9:47,397,460
INFO	2016-11-02 08:58:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:19	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    2s.  Last read position: chr9:57,585,148
INFO	2016-11-02 08:58:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:22	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:06:41s.  Time for last 1,000,000:    2s.  Last read position: chr9:63,772,420
INFO	2016-11-02 08:58:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:24	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:06:43s.  Time for last 1,000,000:    2s.  Last read position: chr9:71,664,937
INFO	2016-11-02 08:58:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:28	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    3s.  Last read position: chr9:85,189,790
INFO	2016-11-02 08:58:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:30	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    2s.  Last read position: chr9:100,454,664
INFO	2016-11-02 08:58:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:33	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    2s.  Last read position: chr9:108,447,680
INFO	2016-11-02 08:58:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:35	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    2s.  Last read position: chr9:117,321,555
INFO	2016-11-02 08:58:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:38	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    2s.  Last read position: chr10:4,270,957
INFO	2016-11-02 08:58:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:41	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    2s.  Last read position: chr10:19,596,797
INFO	2016-11-02 08:58:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:43	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    2s.  Last read position: chr10:38,588,805
INFO	2016-11-02 08:58:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:45	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:07:05s.  Time for last 1,000,000:    2s.  Last read position: chr10:52,095,217
INFO	2016-11-02 08:58:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:48	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    2s.  Last read position: chr10:62,792,064
INFO	2016-11-02 08:58:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:51	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:07:10s.  Time for last 1,000,000:    2s.  Last read position: chr10:75,561,885
INFO	2016-11-02 08:58:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:58:57	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:07:17s.  Time for last 1,000,000:    6s.  Last read position: chr10:80,494,807
INFO	2016-11-02 08:58:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:00	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    2s.  Last read position: chr10:85,828,845
INFO	2016-11-02 08:59:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:02	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    2s.  Last read position: chr10:96,624,020
INFO	2016-11-02 08:59:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:05	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    3s.  Last read position: chr10:117,432,357
INFO	2016-11-02 08:59:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:08	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    2s.  Last read position: chr10:127,674,739
INFO	2016-11-02 08:59:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:10	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    2s.  Last read position: chr11:6,541,277
INFO	2016-11-02 08:59:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:13	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    2s.  Last read position: chr11:22,982,409
INFO	2016-11-02 08:59:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:16	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:07:35s.  Time for last 1,000,000:    3s.  Last read position: chr11:35,822,060
INFO	2016-11-02 08:59:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:19	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    2s.  Last read position: chr11:50,776,166
INFO	2016-11-02 08:59:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:21	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:07:40s.  Time for last 1,000,000:    2s.  Last read position: chr11:58,192,621
INFO	2016-11-02 08:59:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:24	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    2s.  Last read position: chr11:65,507,556
INFO	2016-11-02 08:59:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:26	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    2s.  Last read position: chr11:72,070,297
INFO	2016-11-02 08:59:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:29	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    2s.  Last read position: chr11:78,019,759
INFO	2016-11-02 08:59:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:31	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:07:51s.  Time for last 1,000,000:    2s.  Last read position: chr11:84,653,948
INFO	2016-11-02 08:59:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:34	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:07:53s.  Time for last 1,000,000:    2s.  Last read position: chr11:94,823,479
INFO	2016-11-02 08:59:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:41	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    7s.  Last read position: chr11:98,834,846
INFO	2016-11-02 08:59:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:44	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    2s.  Last read position: chr11:103,272,232
INFO	2016-11-02 08:59:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:46	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:08:06s.  Time for last 1,000,000:    2s.  Last read position: chr11:110,476,776
INFO	2016-11-02 08:59:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:49	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    2s.  Last read position: chr11:117,180,002
INFO	2016-11-02 08:59:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:51	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:08:10s.  Time for last 1,000,000:    2s.  Last read position: chr11:120,808,742
INFO	2016-11-02 08:59:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:54	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    2s.  Last read position: chr12:16,053,147
INFO	2016-11-02 08:59:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:56	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    2s.  Last read position: chr12:33,368,460
INFO	2016-11-02 08:59:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:59:59	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    2s.  Last read position: chr12:55,492,203
INFO	2016-11-02 08:59:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:01	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    2s.  Last read position: chr12:74,013,741
INFO	2016-11-02 09:00:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:03	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    2s.  Last read position: chr12:83,773,539
INFO	2016-11-02 09:00:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:06	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    2s.  Last read position: chr12:98,371,200
INFO	2016-11-02 09:00:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:08	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    2s.  Last read position: chr12:105,858,720
INFO	2016-11-02 09:00:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:13	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    4s.  Last read position: chr12:112,928,492
INFO	2016-11-02 09:00:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:16	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    2s.  Last read position: chr13:13,583,805
INFO	2016-11-02 09:00:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:24	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:08:43s.  Time for last 1,000,000:    8s.  Last read position: chr13:29,823,639
INFO	2016-11-02 09:00:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:26	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:    2s.  Last read position: chr13:41,302,952
INFO	2016-11-02 09:00:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:29	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    3s.  Last read position: chr13:49,298,685
INFO	2016-11-02 09:00:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:33	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:08:52s.  Time for last 1,000,000:    4s.  Last read position: chr13:56,041,930
INFO	2016-11-02 09:00:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:36	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    3s.  Last read position: chr13:71,161,784
INFO	2016-11-02 09:00:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:39	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    3s.  Last read position: chr13:92,641,822
INFO	2016-11-02 09:00:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:43	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    3s.  Last read position: chr13:103,708,214
INFO	2016-11-02 09:00:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:46	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    3s.  Last read position: chr13:119,283,695
INFO	2016-11-02 09:00:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:50	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    4s.  Last read position: chr14:21,831,195
INFO	2016-11-02 09:00:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:53	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:09:12s.  Time for last 1,000,000:    3s.  Last read position: chr14:31,581,383
INFO	2016-11-02 09:00:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:00:56	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:09:16s.  Time for last 1,000,000:    3s.  Last read position: chr14:49,072,427
INFO	2016-11-02 09:00:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:00	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    3s.  Last read position: chr14:59,564,938
INFO	2016-11-02 09:01:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:03	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    3s.  Last read position: chr14:68,789,211
INFO	2016-11-02 09:01:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:09	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    5s.  Last read position: chr14:78,930,993
INFO	2016-11-02 09:01:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:11	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:09:30s.  Time for last 1,000,000:    2s.  Last read position: chr14:105,898,896
INFO	2016-11-02 09:01:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:18	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:09:37s.  Time for last 1,000,000:    7s.  Last read position: chr15:5,242,315
INFO	2016-11-02 09:01:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:21	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    2s.  Last read position: chr15:27,755,022
INFO	2016-11-02 09:01:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:23	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:    2s.  Last read position: chr15:44,748,599
INFO	2016-11-02 09:01:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:26	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:09:45s.  Time for last 1,000,000:    2s.  Last read position: chr15:63,719,662
INFO	2016-11-02 09:01:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:28	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:09:47s.  Time for last 1,000,000:    2s.  Last read position: chr15:75,550,011
INFO	2016-11-02 09:01:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:30	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    2s.  Last read position: chr15:79,834,804
INFO	2016-11-02 09:01:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:33	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:    2s.  Last read position: chr15:84,770,042
INFO	2016-11-02 09:01:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:35	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:    2s.  Last read position: chr15:95,793,100
INFO	2016-11-02 09:01:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:38	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    2s.  Last read position: chr15:100,984,073
INFO	2016-11-02 09:01:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:40	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    2s.  Last read position: chr16:7,383,376
INFO	2016-11-02 09:01:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:43	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    2s.  Last read position: chr16:17,210,501
INFO	2016-11-02 09:01:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:45	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:10:04s.  Time for last 1,000,000:    2s.  Last read position: chr16:25,177,590
INFO	2016-11-02 09:01:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:47	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    2s.  Last read position: chr16:35,061,200
INFO	2016-11-02 09:01:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:54	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:10:13s.  Time for last 1,000,000:    6s.  Last read position: chr16:50,239,643
INFO	2016-11-02 09:01:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:01:57	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:10:16s.  Time for last 1,000,000:    2s.  Last read position: chr16:76,588,906
INFO	2016-11-02 09:01:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:07	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:   10s.  Last read position: chr16:93,223,390
INFO	2016-11-02 09:02:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:11	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    3s.  Last read position: chr17:6,861,631
INFO	2016-11-02 09:02:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:15	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    4s.  Last read position: chr17:23,840,649
INFO	2016-11-02 09:02:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:20	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:10:39s.  Time for last 1,000,000:    4s.  Last read position: chr17:28,106,612
INFO	2016-11-02 09:02:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:23	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:10:42s.  Time for last 1,000,000:    3s.  Last read position: chr17:32,788,162
INFO	2016-11-02 09:02:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:27	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:    3s.  Last read position: chr17:39,843,971
INFO	2016-11-02 09:02:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:31	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:10:50s.  Time for last 1,000,000:    3s.  Last read position: chr17:46,298,772
INFO	2016-11-02 09:02:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:35	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:10:54s.  Time for last 1,000,000:    3s.  Last read position: chr17:56,250,711
INFO	2016-11-02 09:02:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:39	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:10:58s.  Time for last 1,000,000:    3s.  Last read position: chr17:70,734,206
INFO	2016-11-02 09:02:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:43	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:11:02s.  Time for last 1,000,000:    3s.  Last read position: chr17:83,242,375
INFO	2016-11-02 09:02:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:46	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    3s.  Last read position: chr17:94,886,610
INFO	2016-11-02 09:02:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:50	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:11:10s.  Time for last 1,000,000:    4s.  Last read position: chr18:21,591,873
INFO	2016-11-02 09:02:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:02:54	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    4s.  Last read position: chr18:35,829,380
INFO	2016-11-02 09:02:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:00	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:11:19s.  Time for last 1,000,000:    5s.  Last read position: chr18:49,833,210
INFO	2016-11-02 09:03:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:08	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:11:27s.  Time for last 1,000,000:    7s.  Last read position: chr18:63,131,149
INFO	2016-11-02 09:03:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:10	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:11:29s.  Time for last 1,000,000:    2s.  Last read position: chr18:75,217,491
INFO	2016-11-02 09:03:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:12	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:11:32s.  Time for last 1,000,000:    2s.  Last read position: chr18:84,390,154
INFO	2016-11-02 09:03:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:15	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:    2s.  Last read position: chr19:7,235,212
INFO	2016-11-02 09:03:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:17	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:11:37s.  Time for last 1,000,000:    2s.  Last read position: chr19:18,672,483
INFO	2016-11-02 09:03:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:20	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:11:39s.  Time for last 1,000,000:    2s.  Last read position: chr19:32,470,266
INFO	2016-11-02 09:03:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:22	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:11:42s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,776,889
INFO	2016-11-02 09:03:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:25	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    2s.  Last read position: chr19:49,555,835
INFO	2016-11-02 09:03:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:27	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:11:47s.  Time for last 1,000,000:    2s.  Last read position: chr19:61,224,427
INFO	2016-11-02 09:03:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:30	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:11:49s.  Time for last 1,000,000:    2s.  Last read position: chrX:52,852,459
INFO	2016-11-02 09:03:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:32	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:11:52s.  Time for last 1,000,000:    2s.  Last read position: chrX:103,433,007
INFO	2016-11-02 09:03:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:35	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:11:54s.  Time for last 1,000,000:    2s.  Last read position: chrX:159,803,720
INFO	2016-11-02 09:03:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 09:03:36	MarkDuplicates	Read 202537199 records. 0 pairs never matched.
INFO	2016-11-02 09:03:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3264292680; totalMemory: 3350724608; maxMemory: 3817865216
INFO	2016-11-02 09:03:40	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 09:03:41	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 09:03:41	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 09:05:09	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 09:05:14	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3334003280; totalMemory: 3362258944; maxMemory: 3817865216
INFO	2016-11-02 09:05:14	MarkDuplicates	Marking 188354092 records as duplicates.
INFO	2016-11-02 09:05:14	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 09:06:50	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:36s.  Time for last 10,000,000:   96s.  Last read position: chr1:156,954,449
INFO	2016-11-02 09:08:10	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:56s.  Time for last 10,000,000:   80s.  Last read position: chr2:75,832,400
INFO	2016-11-02 09:09:32	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:17s.  Time for last 10,000,000:   81s.  Last read position: chr3:3,031,693
INFO	2016-11-02 09:10:52	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:38s.  Time for last 10,000,000:   80s.  Last read position: chr4:5,034,196
INFO	2016-11-02 09:12:13	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:59s.  Time for last 10,000,000:   80s.  Last read position: chr4:136,897,865
INFO	2016-11-02 09:13:34	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:20s.  Time for last 10,000,000:   81s.  Last read position: chr5:112,890,689
INFO	2016-11-02 09:15:06	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:51s.  Time for last 10,000,000:   91s.  Last read position: chr6:71,440,911
INFO	2016-11-02 09:16:38	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:24s.  Time for last 10,000,000:   92s.  Last read position: chr7:36,473,353
INFO	2016-11-02 09:18:05	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:51s.  Time for last 10,000,000:   86s.  Last read position: chr8:3,460,329
INFO	2016-11-02 09:19:33	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:14:19s.  Time for last 10,000,000:   88s.  Last read position: chr8:124,239,255
INFO	2016-11-02 09:20:59	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:15:44s.  Time for last 10,000,000:   85s.  Last read position: chr9:108,447,680
INFO	2016-11-02 09:22:34	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:17:20s.  Time for last 10,000,000:   95s.  Last read position: chr10:96,624,020
INFO	2016-11-02 09:24:18	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:19:04s.  Time for last 10,000,000:  103s.  Last read position: chr11:78,019,759
INFO	2016-11-02 09:25:47	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:20:32s.  Time for last 10,000,000:   88s.  Last read position: chr12:55,492,203
INFO	2016-11-02 09:27:17	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:22:02s.  Time for last 10,000,000:   89s.  Last read position: chr13:56,041,930
INFO	2016-11-02 09:28:46	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:23:31s.  Time for last 10,000,000:   89s.  Last read position: chr14:78,930,993
INFO	2016-11-02 09:30:10	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:24:55s.  Time for last 10,000,000:   83s.  Last read position: chr15:100,984,073
INFO	2016-11-02 09:31:48	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:26:34s.  Time for last 10,000,000:   98s.  Last read position: chr17:28,106,612
INFO	2016-11-02 09:33:30	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:28:15s.  Time for last 10,000,000:  101s.  Last read position: chr18:49,833,210
INFO	2016-11-02 09:34:56	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:29:41s.  Time for last 10,000,000:   85s.  Last read position: chrX:52,852,459
Could not delete file /tmp/imk1/sortingcollection.9025278292607238043.tmp
Could not delete file /tmp/imk1/sortingcollection.1757540737134334588.tmp
INFO	2016-11-02 09:35:16	MarkDuplicates	Before output close freeMemory: 3394639696; totalMemory: 3425173504; maxMemory: 3817865216
INFO	2016-11-02 09:35:17	MarkDuplicates	After output close freeMemory: 3394638880; totalMemory: 3425173504; maxMemory: 3817865216
[Wed Nov 02 09:35:18 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 43.63 minutes.
Runtime.totalMemory()=3425173504

 

 
# 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/SRR836456/out/align/rep1/SRR836456.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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/SRR836456/out/qc/rep1/SRR836456.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--------------------
11860 (process ID) old priority 0, new priority 10

  

 
# 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/SRR836456/out/align/rep1/SRR836456.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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--------------------
50726 (process ID) old priority 0, new priority 10

Waiting for 31 seconds.

  

 
# 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/SRR836456/out/align/rep1/SRR836456.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.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--------------------
50825 (process ID) old priority 0, new priority 10
Waiting for 34 seconds.

  

 
# 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/SRR836456/out/align/rep1/SRR836456.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/SRR836456/out/align/rep1/SRR836456.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/rep1/SRR836456.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr2/SRR836456.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/align/pseudo_reps/rep1/pr1/SRR836456.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--------------------
50820 (process ID) old priority 0, new priority 10
Waiting for 34 seconds.

  

 
# 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/SRR836456/out/align/rep1/SRR836456.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/out/qc/rep1/SRR836456.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--------------------
17025 (process ID) old priority 0, new priority 10

  
--------------------Post mortem info--------------------
==============================================================
job_number:                 3349
exec_file:                  job_scripts/3349
submission_time:            Wed Nov  2 09:58:26 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456/chipseq.bds.20161101_222022_418_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stdout.cluster
jobshare:                   0
env_list:                   MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 51178 22,USER=imk1,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/18,LOGNAME=imk1,_=/usr/bin/bds,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect,PERL5LIB=/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5,DISPLAY=localhost:12.0,SGE_CELL=default,STY=34348.SRR836456.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_rUZelg,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836456,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 51178 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
parallel environment:  shm range: 4
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            queue instance "q@mitra" dropped because it is temporarily not available
                            queue instance "amd.q@mitra" dropped because it is temporarily not available
                            queue instance "q@wotan" dropped because it is full
                            queue instance "amd.q@surya" dropped because it is full
                            queue instance "amd.q@kadru" dropped because it is full
                            queue instance "amd.q@kali" dropped because it is full
                            queue instance "amd.q@nandi" dropped because it is full
                            queue instance "amd.q@wotan" dropped because it is full