xcor rep1

 chipseq.bds.20161101_222024_463_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10
chipseq.bds.20161101_222024_463_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20161101_222024_463_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20161101_222024_463_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15
chipseq.bds.20161101_222024_463_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20161101_222024_463_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17
 

 chipseq.bds.20161101_222024_463_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11
chipseq.bds.20161101_222024_463_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20161101_222024_463_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20161101_222024_463_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 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/SRR836474/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--------------------
30982 (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... 52.70 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... 52.40 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... 51.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.97 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... 46.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.58 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... 45.90 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... 46.17 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... 47.18 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... 49.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.64 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... 53.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.61 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... 44.45 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.31 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... 45.31 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... 47.99 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... 48.74 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.61 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... 46.64 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... 47.20 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... 45.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.58 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... 45.59 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... 47.89 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... 54.98 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... 62.18 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... 61.01 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... 56.14 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... 52.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.94 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... 47.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.72 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... 43.18 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... 41.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.51 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... 40.93 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... 41.73 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... 42.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.13 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... 40.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.67 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.37 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... 48.20 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... 46.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.51 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... 43.32 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... 41.48 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... 39.55 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... 39.89 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... 42.66 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.27 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... 42.15 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... 42.93 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.90 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.53 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... 41.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.38 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.02 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... 52.88 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... 50.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.20 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... 45.54 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... 44.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.52 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... 43.54 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... 45.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.68 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... 44.95 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.52 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... 46.68 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... 52.16 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.75 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.80 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... 55.95 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... 52.14 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... 49.48 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.32 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... 44.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.67 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... 45.45 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... 46.02 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... 45.73 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... 45.55 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... 44.89 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... 46.44 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.24 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... 45.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.84 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... 50.08 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... 53.20 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... 54.84 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... 51.20 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... 49.22 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.97 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... 48.04 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... 48.79 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.71 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... 49.91 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.93 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: 5831.503 sec; CPU: 5832.456 sec

 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836474.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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--------------------
45983 (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] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.61 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 13.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.80 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.72 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.76 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.91 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.77 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 13.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.22 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 13.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 13.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 6.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 195682776 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/SRR836474.fastq.gz
[main] Real time: 16613.319 sec; CPU: 63067.324 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/SRR836474/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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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--------------------
52344 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.01 sec
[bwa_aln_core] refine gapped alignments... 3.15 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.52 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.53 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.43 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.66 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.07 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.25 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.20 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.67 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.24 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 7.70 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.72 sec
[bwa_aln_core] refine gapped alignments... 6.74 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.69 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.56 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 5505024 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... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.64 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.77 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.76 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.44 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.21 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.33 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.83 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.24 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.72 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.69 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.55 sec
[bwa_aln_core] refine gapped alignments... 2.78 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.18 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.74 sec
[bwa_aln_core] refine gapped alignments... 3.24 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.16 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.36 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.12 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.62 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.42 sec
[bwa_aln_core] refine gapped alignments... 8.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.05 sec
[bwa_aln_core] refine gapped alignments... 2.07 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.26 sec
[bwa_aln_core] refine gapped alignments... 2.31 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... 28.34 sec
[bwa_aln_core] refine gapped alignments... 1.71 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.62 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.84 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.48 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.34 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.14 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.88 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.62 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.60 sec
[bwa_aln_core] refine gapped alignments... 3.52 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.71 sec
[bwa_aln_core] refine gapped alignments... 4.96 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.43 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.74 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.50 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.68 sec
[bwa_aln_core] refine gapped alignments... 0.42 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... 23.90 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.79 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.09 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.13 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.55 sec
[bwa_aln_core] refine gapped alignments... 1.74 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... 24.31 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.70 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 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... 25.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.01 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.49 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.74 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.17 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.57 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.83 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.81 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.07 sec
[bwa_aln_core] refine gapped alignments... 2.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.46 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.99 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.99 sec
[bwa_aln_core] refine gapped alignments... 2.84 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.03 sec
[bwa_aln_core] refine gapped alignments... 0.95 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.16 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.40 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.79 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.82 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.61 sec
[bwa_aln_core] refine gapped alignments... 2.08 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.95 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.81 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.56 sec
[bwa_aln_core] refine gapped alignments... 5.79 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.67 sec
[bwa_aln_core] refine gapped alignments... 1.87 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.08 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.14 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.60 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.63 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.07 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.11 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.87 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.14 sec
[bwa_aln_core] refine gapped alignments... 5.37 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.37 sec
[bwa_aln_core] refine gapped alignments... 4.84 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.60 sec
[bwa_aln_core] refine gapped alignments... 2.06 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.16 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.70 sec
[bwa_aln_core] refine gapped alignments... 5.75 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.21 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.47 sec
[bwa_aln_core] refine gapped alignments... 4.88 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.15 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.82 sec
[bwa_aln_core] refine gapped alignments... 2.37 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... 37.00 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.96 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.12 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.49 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.35 sec
[bwa_aln_core] refine gapped alignments... 2.90 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/SRR836474/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: 3636.330 sec; CPU: 3495.100 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/SRR836474/out/align/rep1/SRR836474.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836474.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.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--------------------
7956 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.46 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.16 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.69 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.71 sec
[bwa_aln_core] refine gapped alignments... 1.79 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.52 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.19 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.57 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.41 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.37 sec
[bwa_aln_core] refine gapped alignments... 1.29 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.43 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.71 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.83 sec
[bwa_aln_core] refine gapped alignments... 1.26 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.32 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.58 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.25 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.43 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.31 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.81 sec
[bwa_aln_core] refine gapped alignments... 1.48 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.08 sec
[bwa_aln_core] refine gapped alignments... 1.48 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.56 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.79 sec
[bwa_aln_core] refine gapped alignments... 1.29 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 1.87 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.72 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.18 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.70 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.05 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.46 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.37 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.46 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.98 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.73 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 1.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.01 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.36 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.49 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.23 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.14 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.74 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.49 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.67 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.97 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.20 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.04 sec
[bwa_aln_core] refine gapped alignments... 1.79 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.63 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.54 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.35 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.82 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.56 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.36 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.57 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.98 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.53 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.16 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.29 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.25 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.32 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.68 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.76 sec
[bwa_aln_core] refine gapped alignments... 1.71 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.46 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.36 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.46 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.41 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.68 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.71 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.10 sec
[bwa_aln_core] refine gapped alignments... 1.46 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.35 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.78 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.18 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.27 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.38 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.63 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.44 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.90 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.65 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.02 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.84 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.43 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.76 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.09 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.10 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.68 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.01 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.02 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.94 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.15 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.52 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.16 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.15 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.45 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.89 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.55 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.01 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.11 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.92 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.38 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.05 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.31 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.04 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.81 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.48 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.77 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.47 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.61 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.36 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.65 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.56 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.54 sec
[bwa_aln_core] refine gapped alignments... 3.05 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.89 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.54 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.45 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.74 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.95 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.34 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.21 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.64 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.71 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.18 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.19 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.15 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 2.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.09 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.15 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.64 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.15 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.98 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.15 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 1.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.06 sec
[bwa_aln_core] refine gapped alignments... 1.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.71 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.98 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 1.44 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.74 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.31 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.72 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.83 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.00 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.89 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.68 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.89 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.47 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.68 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.71 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.69 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.23 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.32 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.11 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.73 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.26 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.67 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.83 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.09 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.42 sec
[bwa_aln_core] refine gapped alignments... 1.56 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 1.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.33 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.21 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.9% 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... 0.28 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.28 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.69 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.94 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.49 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.54 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.37 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.79 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.88 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.46 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.17 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.20 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.69 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.63 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.26 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.90 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.96 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.40 sec
[bwa_aln_core] refine gapped alignments... 1.79 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 3.27 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.83 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.68 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.96 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.87 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.62 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.43 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.49 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.50 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.29 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.05 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.53 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.55 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.15 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.69 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.19 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.04 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.57 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.21 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.82 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.24 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.17 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.96 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.7% 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... 0.27 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.44 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.92 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.28 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.71 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.25 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.42 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.65 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.78 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.13 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.57 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.31 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.16 sec
[bwa_aln_core] refine gapped alignments... 0.91 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.14 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.33 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.69 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.12 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.19 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.01 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.38 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.11 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.86 sec
[bwa_aln_core] refine gapped alignments... 1.71 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.83 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.05 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.39 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 1.82 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.38 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.21 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.89 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.41 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.01 sec
[bwa_aln_core] refine gapped alignments... 1.72 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.74 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.95 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 1.72 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.09 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.57 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.45 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.35 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.99 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.00 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.00 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.00 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.00 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.19 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.05 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.14 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.06 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.09 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.07 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.41 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.69 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.38 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.77 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.37 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.24 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.43 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 195682776 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/SRR836474/out/align/rep1/SRR836474.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836474.fastq.gz
[main] Real time: 6235.748 sec; CPU: 5892.776 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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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--------------------
26488 (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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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--------------------
26802 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 03:19:24 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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 03:19:24 PDT 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 03:19:24	MarkDuplicates	Start of doWork freeMemory: 254881632; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 03:19:24	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 03:19:24	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 03:19:30	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 03:19:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:34	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    4s.  Last read position: chr2:120,600,340
INFO	2016-11-02 03:19:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:39	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    4s.  Last read position: chr3:96,659,413
INFO	2016-11-02 03:19:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:43	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    3s.  Last read position: chr4:108,195,091
INFO	2016-11-02 03:19:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:48	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    4s.  Last read position: chr5:103,594,339
INFO	2016-11-02 03:19:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:51	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    2s.  Last read position: chr6:98,592,333
INFO	2016-11-02 03:19:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:54	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    3s.  Last read position: chr7:114,109,505
INFO	2016-11-02 03:19:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:19:58	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:    4s.  Last read position: chr8:121,515,352
INFO	2016-11-02 03:19:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:01	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr10:14,536,964
INFO	2016-11-02 03:20:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:04	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr11:32,924,585
INFO	2016-11-02 03:20:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:09	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr12:41,050,039
INFO	2016-11-02 03:20:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:11	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr13:80,878,598
INFO	2016-11-02 03:20:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:15	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    3s.  Last read position: chr15:12,027,335
INFO	2016-11-02 03:20:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:18	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    2s.  Last read position: chr16:56,024,589
INFO	2016-11-02 03:20:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:33	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:   15s.  Last read position: chr18:10,030,498
INFO	2016-11-02 03:20:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:36	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    2s.  Last read position: chrX:36,565,109
INFO	2016-11-02 03:20:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:20:38	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 03:20:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2542323536; totalMemory: 2628780032; maxMemory: 3817865216
INFO	2016-11-02 03:20:39	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 03:20:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 03:20:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 03:20:43	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 03:20:44	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1984215792; totalMemory: 2965897216; maxMemory: 3817865216
INFO	2016-11-02 03:20:44	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 03:20:44	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 03:21:58	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 03:22:48	MarkDuplicates	Before output close freeMemory: 2941147720; totalMemory: 2970091520; maxMemory: 3817865216
INFO	2016-11-02 03:22:50	MarkDuplicates	After output close freeMemory: 2960021032; totalMemory: 2988965888; maxMemory: 3817865216
[Wed Nov 02 03:22:50 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.44 minutes.
Runtime.totalMemory()=2988965888

 

 
# 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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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/SRR836474/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/SRR836474/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/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/SRR836474/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/SRR836474/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--------------------
27273 (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/SRR836474/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/SRR836474/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--------------------
27524 (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/SRR836474/out/align/rep1/SRR836474.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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/SRR836474/out/align/rep1/SRR836474.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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--------------------
11594 (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/SRR836474/out/align/rep1/SRR836474.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.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--------------------
15160 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 08:41:16 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.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 08:41:16 PDT 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 08:41:16	MarkDuplicates	Start of doWork freeMemory: 254882272; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 08:41:16	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 08:41:16	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 08:41:16	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836474.7991095'.  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 08:41:20	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr1:34,251,374
INFO	2016-11-02 08:41:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:23	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    3s.  Last read position: chr1:60,030,044
INFO	2016-11-02 08:41:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:27	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    3s.  Last read position: chr1:87,393,069
INFO	2016-11-02 08:41:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:30	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    3s.  Last read position: chr1:116,449,676
INFO	2016-11-02 08:41:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:33	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    2s.  Last read position: chr1:142,408,349
INFO	2016-11-02 08:41:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    2s.  Last read position: chr1:165,839,830
INFO	2016-11-02 08:41:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:38	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    2s.  Last read position: chr1:191,006,666
INFO	2016-11-02 08:41:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    4s.  Last read position: chr2:24,877,553
INFO	2016-11-02 08:41:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:48	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr2:46,552,289
INFO	2016-11-02 08:41:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:53	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    4s.  Last read position: chr2:71,951,649
INFO	2016-11-02 08:41:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:56	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr2:97,434,877
INFO	2016-11-02 08:41:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:41:59	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    2s.  Last read position: chr2:120,957,801
INFO	2016-11-02 08:41:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:01	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    2s.  Last read position: chr2:145,957,526
INFO	2016-11-02 08:42:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:04	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr2:169,917,938
INFO	2016-11-02 08:42:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:16	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:   12s.  Last read position: chr3:23,916,592
INFO	2016-11-02 08:42:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:19	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    2s.  Last read position: chr3:53,526,624
INFO	2016-11-02 08:42:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:21	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    2s.  Last read position: chr3:81,325,957
INFO	2016-11-02 08:42:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:24	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    2s.  Last read position: chr3:104,145,956
INFO	2016-11-02 08:42:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:27	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    2s.  Last read position: chr3:129,213,983
INFO	2016-11-02 08:42:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:29	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    2s.  Last read position: chr3:153,531,445
INFO	2016-11-02 08:42:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:33	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:17s.  Time for last 1,000,000:    3s.  Last read position: chr4:26,629,552
INFO	2016-11-02 08:42:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:38	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    4s.  Last read position: chr4:53,716,943
INFO	2016-11-02 08:42:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:41	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    2s.  Last read position: chr4:85,047,509
INFO	2016-11-02 08:42:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:44	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    3s.  Last read position: chr4:112,110,454
INFO	2016-11-02 08:42:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:47	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:    3s.  Last read position: chr4:135,725,919
INFO	2016-11-02 08:42:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:50	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    2s.  Last read position: chr5:9,217,617
INFO	2016-11-02 08:42:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:52	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr5:37,786,379
INFO	2016-11-02 08:42:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:55	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:    2s.  Last read position: chr5:65,935,564
INFO	2016-11-02 08:42:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:42:59	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:    4s.  Last read position: chr5:96,111,626
INFO	2016-11-02 08:42:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:05	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    5s.  Last read position: chr5:121,509,629
INFO	2016-11-02 08:43:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:07	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:50s.  Time for last 1,000,000:    2s.  Last read position: chr5:146,777,939
INFO	2016-11-02 08:43:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:09	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    2s.  Last read position: chr6:25,288,805
INFO	2016-11-02 08:43:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:12	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    2s.  Last read position: chr6:50,994,982
INFO	2016-11-02 08:43:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:15	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    2s.  Last read position: chr6:80,145,764
INFO	2016-11-02 08:43:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:18	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr6:106,405,745
INFO	2016-11-02 08:43:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:20	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    2s.  Last read position: chr6:131,983,475
INFO	2016-11-02 08:43:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:23	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    2s.  Last read position: chr7:18,872,433
INFO	2016-11-02 08:43:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:25	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    1s.  Last read position: chr7:51,140,863
INFO	2016-11-02 08:43:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:27	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    2s.  Last read position: chr7:81,155,020
INFO	2016-11-02 08:43:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:29	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    2s.  Last read position: chr7:105,810,930
INFO	2016-11-02 08:43:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:33	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    3s.  Last read position: chr7:130,388,597
INFO	2016-11-02 08:43:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:35	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    2s.  Last read position: chr8:18,061,711
INFO	2016-11-02 08:43:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:37	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    2s.  Last read position: chr8:48,388,180
INFO	2016-11-02 08:43:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:39	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:02:23s.  Time for last 1,000,000:    2s.  Last read position: chr8:76,689,899
INFO	2016-11-02 08:43:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:51	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   12s.  Last read position: chr8:103,687,306
INFO	2016-11-02 08:43:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:54	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:37s.  Time for last 1,000,000:    2s.  Last read position: chr8:128,044,406
INFO	2016-11-02 08:43:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:56	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    2s.  Last read position: chr9:31,655,025
INFO	2016-11-02 08:43:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:43:58	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:    2s.  Last read position: chr9:57,315,017
INFO	2016-11-02 08:43:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:01	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    2s.  Last read position: chr9:79,371,192
INFO	2016-11-02 08:44:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:04	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    3s.  Last read position: chr9:106,332,730
INFO	2016-11-02 08:44:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:06	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:50s.  Time for last 1,000,000:    2s.  Last read position: chr10:11,106,295
INFO	2016-11-02 08:44:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:09	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    2s.  Last read position: chr10:37,339,180
INFO	2016-11-02 08:44:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:11	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    2s.  Last read position: chr10:62,553,701
INFO	2016-11-02 08:44:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:13	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    2s.  Last read position: chr10:85,751,291
INFO	2016-11-02 08:44:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:15	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:    2s.  Last read position: chr10:110,768,027
INFO	2016-11-02 08:44:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:17	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    2s.  Last read position: chr11:6,283,453
INFO	2016-11-02 08:44:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:19	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    2s.  Last read position: chr11:33,036,453
INFO	2016-11-02 08:44:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:23	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    4s.  Last read position: chr11:58,502,794
INFO	2016-11-02 08:44:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:29	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    6s.  Last read position: chr11:79,671,786
INFO	2016-11-02 08:44:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:31	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:101,011,721
INFO	2016-11-02 08:44:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:34	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    2s.  Last read position: chr11:121,404,119
INFO	2016-11-02 08:44:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:36	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    2s.  Last read position: chr12:36,329,326
INFO	2016-11-02 08:44:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:38	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    2s.  Last read position: chr12:65,205,258
INFO	2016-11-02 08:44:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:40	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    2s.  Last read position: chr12:89,808,374
INFO	2016-11-02 08:44:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:42	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    2s.  Last read position: chr12:117,117,156
INFO	2016-11-02 08:44:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:44	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    2s.  Last read position: chr13:27,872,925
INFO	2016-11-02 08:44:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:48	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    3s.  Last read position: chr13:52,675,715
INFO	2016-11-02 08:44:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:50	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    2s.  Last read position: chr13:83,249,482
INFO	2016-11-02 08:44:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:52	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:03:35s.  Time for last 1,000,000:    2s.  Last read position: chr13:108,216,606
INFO	2016-11-02 08:44:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:54	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    2s.  Last read position: chr14:23,493,202
INFO	2016-11-02 08:44:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:57	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    2s.  Last read position: chr14:55,122,176
INFO	2016-11-02 08:44:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:44:59	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    2s.  Last read position: chr14:79,618,654
INFO	2016-11-02 08:44:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:01	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    2s.  Last read position: chr14:106,894,600
INFO	2016-11-02 08:45:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:07	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    5s.  Last read position: chr15:12,468,388
INFO	2016-11-02 08:45:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:09	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    1s.  Last read position: chr15:43,212,789
INFO	2016-11-02 08:45:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:12	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:03:55s.  Time for last 1,000,000:    2s.  Last read position: chr15:70,744,538
INFO	2016-11-02 08:45:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:14	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    2s.  Last read position: chr15:95,592,704
INFO	2016-11-02 08:45:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:16	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    2s.  Last read position: chr16:18,667,677
INFO	2016-11-02 08:45:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:18	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    2s.  Last read position: chr16:42,824,894
INFO	2016-11-02 08:45:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:21	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    2s.  Last read position: chr16:67,519,894
INFO	2016-11-02 08:45:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:23	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    2s.  Last read position: chr16:93,884,070
INFO	2016-11-02 08:45:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:25	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    2s.  Last read position: chr17:27,037,215
INFO	2016-11-02 08:45:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:27	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    2s.  Last read position: chr17:46,800,167
INFO	2016-11-02 08:45:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:29	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    2s.  Last read position: chr17:74,185,108
INFO	2016-11-02 08:45:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:33	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    3s.  Last read position: chr18:8,120,023
INFO	2016-11-02 08:45:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:35	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    2s.  Last read position: chr18:36,618,173
INFO	2016-11-02 08:45:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:37	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    2s.  Last read position: chr18:63,709,150
INFO	2016-11-02 08:45:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:39	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    2s.  Last read position: chr18:90,084,711
INFO	2016-11-02 08:45:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:45	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    5s.  Last read position: chr19:27,604,193
INFO	2016-11-02 08:45:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:48	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:    2s.  Last read position: chr19:50,612,766
INFO	2016-11-02 08:45:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:50	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    2s.  Last read position: chrX:49,601,638
INFO	2016-11-02 08:45:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:52	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:04:35s.  Time for last 1,000,000:    2s.  Last read position: chrX:110,309,628
INFO	2016-11-02 08:45:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:54	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:    2s.  Last read position: chrX:169,397,549
INFO	2016-11-02 08:45:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:45:54	MarkDuplicates	Read 93177504 records. 0 pairs never matched.
INFO	2016-11-02 08:45:55	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2782306544; totalMemory: 2868379648; maxMemory: 3817865216
INFO	2016-11-02 08:45:55	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 08:45:56	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 08:45:56	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 08:46:16	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 08:46:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1804134800; totalMemory: 2785542144; maxMemory: 3817865216
INFO	2016-11-02 08:46:18	MarkDuplicates	Marking 73893102 records as duplicates.
INFO	2016-11-02 08:46:18	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 08:47:20	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:01s.  Time for last 10,000,000:   61s.  Last read position: chr2:71,951,649
INFO	2016-11-02 08:48:23	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:05s.  Time for last 10,000,000:   63s.  Last read position: chr3:153,531,445
INFO	2016-11-02 08:49:28	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:03:10s.  Time for last 10,000,000:   64s.  Last read position: chr5:121,509,629
INFO	2016-11-02 08:50:32	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:04:14s.  Time for last 10,000,000:   63s.  Last read position: chr7:105,810,930
INFO	2016-11-02 08:51:37	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:05:19s.  Time for last 10,000,000:   65s.  Last read position: chr9:106,332,730
INFO	2016-11-02 08:52:41	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:06:23s.  Time for last 10,000,000:   64s.  Last read position: chr11:101,011,721
INFO	2016-11-02 08:53:46	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:07:28s.  Time for last 10,000,000:   64s.  Last read position: chr14:23,493,202
INFO	2016-11-02 08:54:50	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:08:32s.  Time for last 10,000,000:   64s.  Last read position: chr16:67,519,894
INFO	2016-11-02 08:55:55	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:09:36s.  Time for last 10,000,000:   64s.  Last read position: chr19:50,612,766
INFO	2016-11-02 08:56:15	MarkDuplicates	Before output close freeMemory: 2914920784; totalMemory: 2945449984; maxMemory: 3817865216
INFO	2016-11-02 08:56:16	MarkDuplicates	After output close freeMemory: 2914919728; totalMemory: 2945449984; maxMemory: 3817865216
[Wed Nov 02 08:56:16 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 15.01 minutes.
Runtime.totalMemory()=2945449984

 

 
# 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/SRR836474/out/align/rep1/SRR836474.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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/SRR836474/out/qc/rep1/SRR836474.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--------------------
11710 (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/SRR836474/out/align/rep1/SRR836474.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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--------------------
47429 (process ID) old priority 0, new priority 10

Waiting for 16 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/SRR836474/out/align/rep1/SRR836474.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.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--------------------
47536 (process ID) old priority 0, new priority 10
Waiting for 32 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/SRR836474/out/align/rep1/SRR836474.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/SRR836474/out/align/rep1/SRR836474.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/rep1/SRR836474.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr2/SRR836474.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/align/pseudo_reps/rep1/pr1/SRR836474.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--------------------
47537 (process ID) old priority 0, new priority 10
Waiting for 23 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/SRR836474/out/align/rep1/SRR836474.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/out/qc/rep1/SRR836474.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--------------------
15443 (process ID) old priority 0, new priority 10

  
--------------------Post mortem info--------------------
==============================================================
job_number:                 3333
exec_file:                  job_scripts/3333
submission_time:            Wed Nov  2 09:10:41 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/SRR836474
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836474/chipseq.bds.20161101_222024_463_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/SRR836474/chipseq.bds.20161101_222024_463_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=35834.SRR836474.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/SRR836474,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