xcor rep1

 chipseq.bds.20161101_222023_216_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20161101_222023_216_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20161101_222023_216_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20161101_222023_216_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15
chipseq.bds.20161101_222023_216_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20161101_222023_216_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17
 

 chipseq.bds.20161101_222023_216_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20161101_222023_216_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20161101_222023_216_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836459.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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--------------------
17641 (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] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.36 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.68 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.04 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.24 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.73 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.74 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.06 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.83 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.14 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.84 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.29 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.58 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.71 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.55 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.67 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.68 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.77 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.93 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 196083712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.27 sec
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[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
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[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
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[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.88 sec
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[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.75 sec
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[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.00 sec
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[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
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[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
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[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.65 sec
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[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
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[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
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[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.64 sec
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[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.60 sec
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[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.92 sec
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[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.90 sec
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[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.78 sec
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[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 216793088 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 247690048 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/SRR836459.fastq.gz
[main] Real time: 8193.077 sec; CPU: 29258.756 sec

 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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--------------------
50045 (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... 46.28 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... 44.21 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... 43.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% 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] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% 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] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.05 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... 42.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.66 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... 44.38 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... 46.40 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... 49.92 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... 52.37 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... 49.61 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... 46.26 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... 44.43 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... 42.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.20 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.64 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... 44.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.62 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... 44.48 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... 45.46 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... 44.81 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... 44.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% 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] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.11 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... 54.83 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... 59.51 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... 57.45 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... 53.28 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... 49.81 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... 46.07 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... 45.91 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... 43.73 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... 47.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.11 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.71 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... 44.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.65 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... 44.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.75 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... 50.75 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... 53.99 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... 49.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.42 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... 45.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.73 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... 42.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.54 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... 45.16 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... 45.88 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... 43.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.11 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... 48.69 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... 51.59 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... 51.88 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.39 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... 47.69 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... 45.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.61 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... 45.48 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... 44.97 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... 45.00 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... 45.24 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... 45.19 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... 45.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.64 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... 44.26 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.08 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... 44.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.23 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... 44.93 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... 47.14 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... 51.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.31 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... 50.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.23 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... 46.85 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... 44.11 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... 44.11 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... 45.71 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... 48.07 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... 44.92 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... 46.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.38 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... 45.48 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... 45.46 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.49 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... 44.84 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... 48.07 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.35 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... 47.26 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... 44.93 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... 45.26 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... 46.08 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... 47.13 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... 47.71 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... 48.04 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... 7.67 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: 5772.295 sec; CPU: 5771.136 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/SRR836459/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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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--------------------
19250 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.63 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.88 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.67 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.00 sec
[bwa_aln_core] refine gapped alignments... 0.94 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... 19.16 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.33 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.37 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.45 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.58 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.94 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.00 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.19 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.05 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.52 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.82 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.33 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.03 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.28 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.73 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.29 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.86 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.16 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.07 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 3.01 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.29 sec
[bwa_aln_core] refine gapped alignments... 3.04 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... 18.35 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.10 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.61 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.93 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 1.24 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... 19.08 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.00 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.00 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.89 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.36 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.79 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.29 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.23 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.30 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.68 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.03 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.03 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.80 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.93 sec
[bwa_aln_core] refine gapped alignments... 2.92 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... 18.31 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.22 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.05 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.84 sec
[bwa_aln_core] refine gapped alignments... 3.15 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.78 sec
[bwa_aln_core] refine gapped alignments... 2.83 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.18 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.73 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.35 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.36 sec
[bwa_aln_core] refine gapped alignments... 2.84 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.29 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.89 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 2.98 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.47 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.82 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.48 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.87 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.13 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.84 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.58 sec
[bwa_aln_core] refine gapped alignments... 2.96 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.48 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.02 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.83 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 2.06 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.23 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.00 sec
[bwa_aln_core] refine gapped alignments... 2.93 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... 17.97 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.47 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.63 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.93 sec
[bwa_aln_core] refine gapped alignments... 3.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.46 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.40 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.71 sec
[bwa_aln_core] refine gapped alignments... 1.72 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.06 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.01 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.89 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.88 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.90 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.54 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.43 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.48 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.67 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 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... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.16 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.46 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.51 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.76 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.69 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.50 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.07 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/SRR836459/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: 2494.620 sec; CPU: 2348.928 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/SRR836459/out/align/rep1/SRR836459.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836459.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.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--------------------
17025 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.66 sec
[bwa_aln_core] refine gapped alignments... 3.33 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.40 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.96 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.39 sec
[bwa_aln_core] refine gapped alignments... 1.91 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.09 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.27 sec
[bwa_aln_core] refine gapped alignments... 1.35 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.44 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.20 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.14 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.32 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.10 sec
[bwa_aln_core] refine gapped alignments... 3.95 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.39 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.26 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.02 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.96 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.67 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.90 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.04 sec
[bwa_aln_core] refine gapped alignments... 3.11 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.90 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.95 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.03 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.41 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.44 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.33 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.95 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.08 sec
[bwa_aln_core] refine gapped alignments... 2.83 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.81 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.48 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.28 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.67 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.26 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.33 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.91 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 4.25 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.30 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.45 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.14 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.08 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.83 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.61 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.87 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.15 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.50 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.33 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.57 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.84 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.69 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.28 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.06 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.68 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.84 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.36 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.03 sec
[bwa_aln_core] refine gapped alignments... 1.32 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.54 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.19 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.00 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.81 sec
[bwa_aln_core] refine gapped alignments... 5.29 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 2.91 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.62 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.78 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.63 sec
[bwa_aln_core] refine gapped alignments... 4.89 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.64 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.96 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.83 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.84 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.44 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.75 sec
[bwa_aln_core] refine gapped alignments... 3.35 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.69 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.41 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.63 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.19 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.04 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.47 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.21 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.80 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.80 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.99 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 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] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.45 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.54 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.28 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.89 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 1.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.02 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.45 sec
[bwa_aln_core] refine gapped alignments... 1.58 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.76 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.67 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.38 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.79 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.27 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.47 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.14 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.35 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.48 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.64 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 56623104 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... 0.83 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.89 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.66 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.71 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.67 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.42 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.93 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.59 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 1.66 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.98 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.48 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.74 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.24 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.61 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.29 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.47 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.45 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.79 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.39 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.45 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 3.96 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.04 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.66 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.81 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.51 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.58 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.36 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.80 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.20 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.84 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.16 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.98 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.06 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.59 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.24 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.91 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.84 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.24 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.79 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.97 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.70 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.57 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.69 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.58 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.00 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.97 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.49 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 4.22 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.17 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.93 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.44 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.90 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.93 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.71 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.67 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.69 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.05 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.97 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.29 sec
[bwa_aln_core] refine gapped alignments... 1.52 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.56 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.21 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.98 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.17 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.28 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.92 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.93 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.29 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.87 sec
[bwa_aln_core] refine gapped alignments... 1.93 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.39 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.32 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.28 sec
[bwa_aln_core] refine gapped alignments... 2.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.04 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.52 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.86 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.81 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.69 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.67 sec
[bwa_aln_core] refine gapped alignments... 1.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.90 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.02 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.26 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.03 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.94 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.03 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.11 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.59 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.06 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.77 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.63 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.30 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.4% 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... 0.40 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.57 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.08 sec
[bwa_aln_core] refine gapped alignments... 1.82 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.45 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.27 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.86 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.95 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.19 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.33 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.66 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.56 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.84 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.00 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.17 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.84 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.15 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.87 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.61 sec
[bwa_aln_core] refine gapped alignments... 1.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.48 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.86 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.94 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.03 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.46 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.51 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.92 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.14 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.03 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.74 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.46 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.71 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.43 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.98 sec
[bwa_aln_core] refine gapped alignments... 3.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.22 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.57 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.90 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.01 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.57 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.88 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.16 sec
[bwa_aln_core] refine gapped alignments... 4.85 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.73 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.96 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.04 sec
[bwa_aln_core] refine gapped alignments... 4.13 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.43 sec
[bwa_aln_core] refine gapped alignments... 1.97 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.11 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.04 sec
[bwa_aln_core] refine gapped alignments... 3.28 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.88 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.38 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.69 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.65 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.93 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.38 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.98 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.72 sec
[bwa_aln_core] refine gapped alignments... 1.92 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.75 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.36 sec
[bwa_aln_core] refine gapped alignments... 2.08 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.66 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.42 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.77 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 1.59 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.07 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.64 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.64 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 1.73 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.23 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.82 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.17 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.72 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.85 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.14 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.50 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.51 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.30 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.96 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.85 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.73 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.19 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.24 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.46 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.84 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.29 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.05 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.44 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.61 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.60 sec
[bwa_aln_core] refine gapped alignments... 3.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.86 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.88 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.58 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.86 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.97 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.59 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.73 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.78 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.72 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.45 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.59 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 1.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.91 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.39 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.76 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.71 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.53 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.63 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.64 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.57 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.03 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
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[bwa_aln_core] 196083712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.24 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.72 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
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[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
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[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.59 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.96 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
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[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.08 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
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[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.70 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
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[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
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[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
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[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.94 sec
[bwa_aln_core] refine gapped alignments... 1.61 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.86 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.00 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.49 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.67 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.76 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.19 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.55 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.61 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.91 sec
[bwa_aln_core] refine gapped alignments... 1.94 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.24 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.31 sec
[bwa_aln_core] refine gapped alignments... 0.83 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.88 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.57 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.01 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.84 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.58 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.61 sec
[bwa_aln_core] refine gapped alignments... 1.74 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.60 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.40 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.00 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.15 sec
[bwa_aln_core] refine gapped alignments... 3.01 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.40 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.37 sec
[bwa_aln_core] refine gapped alignments... 3.65 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.62 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.01 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.51 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 216793088 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.12 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.23 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.21 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.02 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.92 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.34 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.53 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.00 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.31 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.13 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.33 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.44 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.67 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.50 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.59 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.10 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.29 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.52 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.46 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.40 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.57 sec
[bwa_aln_core] refine gapped alignments... 3.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.68 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.49 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.14 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.93 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.71 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.74 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.19 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.11 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.24 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.76 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.23 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.91 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.45 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.77 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.91 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.58 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.70 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.19 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.40 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.54 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.72 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.02 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.43 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.30 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 247690048 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/SRR836459/out/align/rep1/SRR836459.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836459.fastq.gz
[main] Real time: 13602.744 sec; CPU: 13097.068 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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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--------------------
29719 (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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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--------------------
28728 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 02:38:09 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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 02:38:09 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 02:38:09	MarkDuplicates	Start of doWork freeMemory: 254881776; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 02:38:09	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 02:38:09	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 02:38:14	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:169,651,309
INFO	2016-11-02 02:38:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:17	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    3s.  Last read position: chr2:120,600,340
INFO	2016-11-02 02:38:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:20	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    3s.  Last read position: chr3:96,659,413
INFO	2016-11-02 02:38:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:24	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    3s.  Last read position: chr4:108,195,091
INFO	2016-11-02 02:38:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:28	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    3s.  Last read position: chr5:103,594,339
INFO	2016-11-02 02:38:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:31	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    3s.  Last read position: chr6:98,592,333
INFO	2016-11-02 02:38:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:36	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    4s.  Last read position: chr7:114,109,505
INFO	2016-11-02 02:38:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:41	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    5s.  Last read position: chr8:121,515,352
INFO	2016-11-02 02:38:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:46	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    5s.  Last read position: chr10:14,536,964
INFO	2016-11-02 02:38:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:49	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    3s.  Last read position: chr11:32,924,585
INFO	2016-11-02 02:38:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:53	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    3s.  Last read position: chr12:41,050,039
INFO	2016-11-02 02:38:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:56	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    3s.  Last read position: chr13:80,878,598
INFO	2016-11-02 02:38:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:59	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    3s.  Last read position: chr15:12,027,335
INFO	2016-11-02 02:38:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:39:03	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:53s.  Time for last 1,000,000:    3s.  Last read position: chr16:56,024,589
INFO	2016-11-02 02:39:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:39:22	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:   18s.  Last read position: chr18:10,030,498
INFO	2016-11-02 02:39:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:39:25	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:15s.  Time for last 1,000,000:    3s.  Last read position: chrX:36,565,109
INFO	2016-11-02 02:39:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:39:27	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 02:39:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1901641344; totalMemory: 1972895744; maxMemory: 3817865216
INFO	2016-11-02 02:39:29	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 02:39:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 02:39:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 02:39:34	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 02:39:34	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1993855024; totalMemory: 2961702912; maxMemory: 3817865216
INFO	2016-11-02 02:39:34	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 02:39:34	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 02:41:09	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:34s.  Time for last 10,000,000:   94s.  Last read position: chr11:32,924,585
INFO	2016-11-02 02:42:14	MarkDuplicates	Before output close freeMemory: 2655507000; totalMemory: 2671247360; maxMemory: 3817865216
INFO	2016-11-02 02:42:15	MarkDuplicates	After output close freeMemory: 2641350168; totalMemory: 2657091584; maxMemory: 3817865216
[Wed Nov 02 02:42:15 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 4.09 minutes.
Runtime.totalMemory()=2657091584

 

 
# 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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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/SRR836459/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/SRR836459/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/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/SRR836459/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/SRR836459/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--------------------
35284 (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/SRR836459/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/SRR836459/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--------------------
25050 (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/SRR836459/out/align/rep1/SRR836459.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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/SRR836459/out/align/rep1/SRR836459.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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--------------------
30282 (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/SRR836459/out/align/rep1/SRR836459.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.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--------------------
10508 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 07:33:25 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.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 07:33:25 PDT 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 07:33:25	MarkDuplicates	Start of doWork freeMemory: 254882264; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 07:33:25	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 07:33:25	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 07:33:26	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836459.15365268'.  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 07:33:34	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:31,112,802
INFO	2016-11-02 07:33:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:33:40	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    5s.  Last read position: chr1:41,150,547
INFO	2016-11-02 07:33:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:33:44	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    4s.  Last read position: chr1:59,314,222
INFO	2016-11-02 07:33:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:33:51	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:24s.  Time for last 1,000,000:    6s.  Last read position: chr1:74,776,052
INFO	2016-11-02 07:33:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:33:55	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    4s.  Last read position: chr1:86,698,947
INFO	2016-11-02 07:33:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:33:58	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    3s.  Last read position: chr1:97,554,341
INFO	2016-11-02 07:33:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:02	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    3s.  Last read position: chr1:125,508,857
INFO	2016-11-02 07:34:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:04	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    2s.  Last read position: chr1:133,946,698
INFO	2016-11-02 07:34:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:07	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr1:147,667,202
INFO	2016-11-02 07:34:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:11	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    4s.  Last read position: chr1:158,766,396
INFO	2016-11-02 07:34:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:13	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr1:170,136,450
INFO	2016-11-02 07:34:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:16	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    2s.  Last read position: chr1:179,450,559
INFO	2016-11-02 07:34:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:19	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chr1:186,958,032
INFO	2016-11-02 07:34:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:24	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    5s.  Last read position: chr2:5,192,467
INFO	2016-11-02 07:34:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:37	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:   12s.  Last read position: chr2:20,894,354
INFO	2016-11-02 07:34:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:39	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    2s.  Last read position: chr2:28,278,253
INFO	2016-11-02 07:34:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:42	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr2:32,220,485
INFO	2016-11-02 07:34:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:47	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:20s.  Time for last 1,000,000:    4s.  Last read position: chr2:38,753,701
INFO	2016-11-02 07:34:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:49	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr2:59,612,860
INFO	2016-11-02 07:34:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:51	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    2s.  Last read position: chr2:72,987,000
INFO	2016-11-02 07:34:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:54	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    2s.  Last read position: chr2:90,474,743
INFO	2016-11-02 07:34:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:34:57	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    3s.  Last read position: chr2:102,186,285
INFO	2016-11-02 07:34:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:00	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    2s.  Last read position: chr2:118,258,307
INFO	2016-11-02 07:35:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:03	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr2:125,424,346
INFO	2016-11-02 07:35:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:05	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    2s.  Last read position: chr2:132,072,717
INFO	2016-11-02 07:35:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:08	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    2s.  Last read position: chr2:148,774,210
INFO	2016-11-02 07:35:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:13	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:46s.  Time for last 1,000,000:    4s.  Last read position: chr2:155,981,334
INFO	2016-11-02 07:35:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:15	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    2s.  Last read position: chr2:163,858,522
INFO	2016-11-02 07:35:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:18	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    2s.  Last read position: chr2:167,775,231
INFO	2016-11-02 07:35:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:24	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    6s.  Last read position: chr2:174,659,488
INFO	2016-11-02 07:35:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:28	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr3:14,381,654
INFO	2016-11-02 07:35:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:30	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    2s.  Last read position: chr3:37,414,508
INFO	2016-11-02 07:35:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:32	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    1s.  Last read position: chr3:57,696,337
INFO	2016-11-02 07:35:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:35	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    2s.  Last read position: chr3:79,567,986
INFO	2016-11-02 07:35:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:37	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:10s.  Time for last 1,000,000:    2s.  Last read position: chr3:88,591,828
INFO	2016-11-02 07:35:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:40	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    3s.  Last read position: chr3:95,964,151
INFO	2016-11-02 07:35:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:42	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    1s.  Last read position: chr3:104,404,086
INFO	2016-11-02 07:35:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:44	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    2s.  Last read position: chr3:116,604,870
INFO	2016-11-02 07:35:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:47	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    2s.  Last read position: chr3:131,118,199
INFO	2016-11-02 07:35:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:49	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    1s.  Last read position: chr3:144,720,224
INFO	2016-11-02 07:35:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:52	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:    3s.  Last read position: chr4:5,548,974
INFO	2016-11-02 07:35:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:54	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    1s.  Last read position: chr4:32,066,964
INFO	2016-11-02 07:35:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:56	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    2s.  Last read position: chr4:44,425,578
INFO	2016-11-02 07:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:35:58	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    1s.  Last read position: chr4:56,288,531
INFO	2016-11-02 07:35:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:03	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chr4:74,516,629
INFO	2016-11-02 07:36:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:05	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    2s.  Last read position: chr4:98,722,599
INFO	2016-11-02 07:36:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:08	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    2s.  Last read position: chr4:109,527,452
INFO	2016-11-02 07:36:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:10	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    1s.  Last read position: chr4:120,081,095
INFO	2016-11-02 07:36:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:12	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    1s.  Last read position: chr4:127,585,252
INFO	2016-11-02 07:36:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:14	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    2s.  Last read position: chr4:133,014,198
INFO	2016-11-02 07:36:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:16	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    1s.  Last read position: chr4:136,090,294
INFO	2016-11-02 07:36:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:19	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:    3s.  Last read position: chr4:141,009,154
INFO	2016-11-02 07:36:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:21	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    1s.  Last read position: chr4:149,724,017
INFO	2016-11-02 07:36:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:23	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    2s.  Last read position: chr4:155,468,420
INFO	2016-11-02 07:36:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:26	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    2s.  Last read position: chr5:23,487,417
INFO	2016-11-02 07:36:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    2s.  Last read position: chr5:32,236,233
INFO	2016-11-02 07:36:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:30	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    2s.  Last read position: chr5:38,781,951
INFO	2016-11-02 07:36:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:34	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:    3s.  Last read position: chr5:64,760,102
INFO	2016-11-02 07:36:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:38	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    4s.  Last read position: chr5:76,980,383
INFO	2016-11-02 07:36:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:40	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    2s.  Last read position: chr5:99,978,268
INFO	2016-11-02 07:36:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:43	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:03:16s.  Time for last 1,000,000:    2s.  Last read position: chr5:110,229,733
INFO	2016-11-02 07:36:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:44	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:03:18s.  Time for last 1,000,000:    1s.  Last read position: chr5:115,559,324
INFO	2016-11-02 07:36:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:47	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:03:20s.  Time for last 1,000,000:    2s.  Last read position: chr5:122,059,852
INFO	2016-11-02 07:36:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:49	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:    1s.  Last read position: chr5:125,534,920
INFO	2016-11-02 07:36:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:52	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    3s.  Last read position: chr5:135,898,361
INFO	2016-11-02 07:36:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:54	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:03:28s.  Time for last 1,000,000:    2s.  Last read position: chr5:140,702,127
INFO	2016-11-02 07:36:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:56	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    1s.  Last read position: chr5:147,399,720
INFO	2016-11-02 07:36:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:36:58	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    1s.  Last read position: chr6:13,838,375
INFO	2016-11-02 07:36:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:00	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    1s.  Last read position: chr6:32,835,125
INFO	2016-11-02 07:37:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:02	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    2s.  Last read position: chr6:47,961,097
INFO	2016-11-02 07:37:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:04	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    1s.  Last read position: chr6:57,615,524
INFO	2016-11-02 07:37:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:08	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:03:41s.  Time for last 1,000,000:    3s.  Last read position: chr6:82,012,141
INFO	2016-11-02 07:37:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:10	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:    1s.  Last read position: chr6:88,491,469
INFO	2016-11-02 07:37:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:15	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    4s.  Last read position: chr6:99,388,150
INFO	2016-11-02 07:37:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:17	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    1s.  Last read position: chr6:114,905,696
INFO	2016-11-02 07:37:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:19	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    2s.  Last read position: chr6:122,669,522
INFO	2016-11-02 07:37:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:21	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    2s.  Last read position: chr6:132,562,142
INFO	2016-11-02 07:37:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:23	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    1s.  Last read position: chr6:145,211,270
INFO	2016-11-02 07:37:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:25	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:    2s.  Last read position: chr7:14,327,249
INFO	2016-11-02 07:37:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:29	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    3s.  Last read position: chr7:24,664,383
INFO	2016-11-02 07:37:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:31	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    2s.  Last read position: chr7:29,556,486
INFO	2016-11-02 07:37:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:33	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    1s.  Last read position: chr7:44,246,764
INFO	2016-11-02 07:37:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:35	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    2s.  Last read position: chr7:49,778,670
INFO	2016-11-02 07:37:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:37	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    2s.  Last read position: chr7:73,348,868
INFO	2016-11-02 07:37:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:39	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:04:13s.  Time for last 1,000,000:    2s.  Last read position: chr7:82,038,714
INFO	2016-11-02 07:37:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:41	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    1s.  Last read position: chr7:98,589,300
INFO	2016-11-02 07:37:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:43	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:    1s.  Last read position: chr7:106,906,696
INFO	2016-11-02 07:37:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:47	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    3s.  Last read position: chr7:117,405,489
INFO	2016-11-02 07:37:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:52	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    4s.  Last read position: chr7:126,421,699
INFO	2016-11-02 07:37:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:54	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    2s.  Last read position: chr7:132,364,910
INFO	2016-11-02 07:37:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:56	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    1s.  Last read position: chr7:141,768,671
INFO	2016-11-02 07:37:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:37:58	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    2s.  Last read position: chr8:11,477,109
INFO	2016-11-02 07:37:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:00	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    2s.  Last read position: chr8:25,623,606
INFO	2016-11-02 07:38:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:03	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    2s.  Last read position: chr8:45,333,195
INFO	2016-11-02 07:38:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:05	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:04:38s.  Time for last 1,000,000:    2s.  Last read position: chr8:69,175,389
INFO	2016-11-02 07:38:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:08	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    3s.  Last read position: chr8:73,905,804
INFO	2016-11-02 07:38:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:10	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    1s.  Last read position: chr8:84,937,485
INFO	2016-11-02 07:38:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:12	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:04:45s.  Time for last 1,000,000:    1s.  Last read position: chr8:94,830,613
INFO	2016-11-02 07:38:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:14	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:04:48s.  Time for last 1,000,000:    2s.  Last read position: chr8:106,893,574
INFO	2016-11-02 07:38:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:16	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    2s.  Last read position: chr8:117,158,150
INFO	2016-11-02 07:38:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:18	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    2s.  Last read position: chr8:122,460,801
INFO	2016-11-02 07:38:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:20	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    1s.  Last read position: chr8:128,181,671
INFO	2016-11-02 07:38:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:25	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    4s.  Last read position: chr9:21,469,191
INFO	2016-11-02 07:38:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:27	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:    2s.  Last read position: chr9:37,230,034
INFO	2016-11-02 07:38:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:29	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:    1s.  Last read position: chr9:45,663,084
INFO	2016-11-02 07:38:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:31	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    2s.  Last read position: chr9:56,994,915
INFO	2016-11-02 07:38:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:33	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    1s.  Last read position: chr9:62,837,569
INFO	2016-11-02 07:38:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:35	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:05:09s.  Time for last 1,000,000:    1s.  Last read position: chr9:70,248,663
INFO	2016-11-02 07:38:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:38	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    2s.  Last read position: chr9:81,917,254
INFO	2016-11-02 07:38:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:40	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    1s.  Last read position: chr9:98,364,548
INFO	2016-11-02 07:38:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:42	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    1s.  Last read position: chr9:107,554,863
INFO	2016-11-02 07:38:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:44	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    2s.  Last read position: chr9:114,754,950
INFO	2016-11-02 07:38:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:46	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    2s.  Last read position: chr9:122,252,333
INFO	2016-11-02 07:38:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:48	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    2s.  Last read position: chr10:15,655,088
INFO	2016-11-02 07:38:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:52	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    3s.  Last read position: chr10:31,297,967
INFO	2016-11-02 07:38:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:54	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:05:28s.  Time for last 1,000,000:    2s.  Last read position: chr10:44,770,125
INFO	2016-11-02 07:38:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:38:56	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:    2s.  Last read position: chr10:61,344,085
INFO	2016-11-02 07:38:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:01	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:    4s.  Last read position: chr10:71,919,594
INFO	2016-11-02 07:39:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:03	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:    1s.  Last read position: chr10:79,926,606
INFO	2016-11-02 07:39:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:05	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    1s.  Last read position: chr10:82,904,247
INFO	2016-11-02 07:39:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:07	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    2s.  Last read position: chr10:93,813,270
INFO	2016-11-02 07:39:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:10	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:05:43s.  Time for last 1,000,000:    2s.  Last read position: chr10:110,455,955
INFO	2016-11-02 07:39:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:14	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    3s.  Last read position: chr10:121,506,354
INFO	2016-11-02 07:39:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:16	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    2s.  Last read position: chr10:129,530,523
INFO	2016-11-02 07:39:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:20	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    3s.  Last read position: chr11:11,686,819
INFO	2016-11-02 07:39:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:22	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    2s.  Last read position: chr11:28,570,834
INFO	2016-11-02 07:39:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:24	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    1s.  Last read position: chr11:44,841,035
INFO	2016-11-02 07:39:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:27	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    2s.  Last read position: chr11:53,293,219
INFO	2016-11-02 07:39:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:29	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    2s.  Last read position: chr11:60,225,051
INFO	2016-11-02 07:39:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:31	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:06:05s.  Time for last 1,000,000:    2s.  Last read position: chr11:69,037,532
INFO	2016-11-02 07:39:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:33	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    1s.  Last read position: chr11:74,547,277
INFO	2016-11-02 07:39:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:35	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:06:08s.  Time for last 1,000,000:    1s.  Last read position: chr11:78,550,827
INFO	2016-11-02 07:39:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:40	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    4s.  Last read position: chr11:85,169,432
INFO	2016-11-02 07:39:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:42	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:06:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:94,482,173
INFO	2016-11-02 07:39:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:45	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    3s.  Last read position: chr11:98,129,645
INFO	2016-11-02 07:39:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:48	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    2s.  Last read position: chr11:101,986,147
INFO	2016-11-02 07:39:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:49	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:06:23s.  Time for last 1,000,000:    1s.  Last read position: chr11:106,776,851
INFO	2016-11-02 07:39:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:52	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    2s.  Last read position: chr11:115,246,710
INFO	2016-11-02 07:39:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:54	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    2s.  Last read position: chr11:118,096,008
INFO	2016-11-02 07:39:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:56	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    2s.  Last read position: chr12:3,305,779
INFO	2016-11-02 07:39:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:39:58	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    2s.  Last read position: chr12:24,975,383
INFO	2016-11-02 07:39:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:00	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    1s.  Last read position: chr12:46,899,044
INFO	2016-11-02 07:40:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:03	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:    2s.  Last read position: chr12:70,199,558
INFO	2016-11-02 07:40:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:05	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:06:38s.  Time for last 1,000,000:    1s.  Last read position: chr12:80,168,837
INFO	2016-11-02 07:40:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:08	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    3s.  Last read position: chr12:87,238,385
INFO	2016-11-02 07:40:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:10	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:06:44s.  Time for last 1,000,000:    1s.  Last read position: chr12:102,705,296
INFO	2016-11-02 07:40:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:16	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    5s.  Last read position: chr12:111,555,453
INFO	2016-11-02 07:40:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:18	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:06:52s.  Time for last 1,000,000:    2s.  Last read position: chr13:5,860,154
INFO	2016-11-02 07:40:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:21	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    2s.  Last read position: chr13:23,903,525
INFO	2016-11-02 07:40:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:24	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    2s.  Last read position: chr13:37,764,439
INFO	2016-11-02 07:40:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:26	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    2s.  Last read position: chr13:47,105,715
INFO	2016-11-02 07:40:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:29	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    2s.  Last read position: chr13:55,210,041
INFO	2016-11-02 07:40:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:33	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: chr13:67,813,847
INFO	2016-11-02 07:40:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:36	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    2s.  Last read position: chr13:90,834,706
INFO	2016-11-02 07:40:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:39	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    2s.  Last read position: chr13:101,758,926
INFO	2016-11-02 07:40:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:41	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:07:15s.  Time for last 1,000,000:    2s.  Last read position: chr13:113,869,595
INFO	2016-11-02 07:40:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:46	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    4s.  Last read position: chr14:20,734,390
INFO	2016-11-02 07:40:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:48	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    2s.  Last read position: chr14:31,684,772
INFO	2016-11-02 07:40:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:50	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:07:23s.  Time for last 1,000,000:    2s.  Last read position: chr14:51,170,527
INFO	2016-11-02 07:40:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:52	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:07:26s.  Time for last 1,000,000:    2s.  Last read position: chr14:60,671,769
INFO	2016-11-02 07:40:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:54	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:    2s.  Last read position: chr14:70,059,308
INFO	2016-11-02 07:40:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:40:59	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    4s.  Last read position: chr14:79,517,372
INFO	2016-11-02 07:40:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:01	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    2s.  Last read position: chr14:108,830,038
INFO	2016-11-02 07:41:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:03	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    2s.  Last read position: chr15:7,129,797
INFO	2016-11-02 07:41:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:05	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:07:39s.  Time for last 1,000,000:    2s.  Last read position: chr15:35,042,441
INFO	2016-11-02 07:41:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:07	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    1s.  Last read position: chr15:58,822,445
INFO	2016-11-02 07:41:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:09	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    1s.  Last read position: chr15:73,673,493
INFO	2016-11-02 07:41:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:13	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    3s.  Last read position: chr15:78,870,023
INFO	2016-11-02 07:41:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:15	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:07:48s.  Time for last 1,000,000:    2s.  Last read position: chr15:82,958,669
INFO	2016-11-02 07:41:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:17	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    1s.  Last read position: chr15:91,718,492
INFO	2016-11-02 07:41:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:19	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:07:52s.  Time for last 1,000,000:    1s.  Last read position: chr15:99,410,712
INFO	2016-11-02 07:41:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:21	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    2s.  Last read position: chr16:3,884,427
INFO	2016-11-02 07:41:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:23	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:07:56s.  Time for last 1,000,000:    2s.  Last read position: chr16:13,830,546
INFO	2016-11-02 07:41:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:25	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:07:59s.  Time for last 1,000,000:    2s.  Last read position: chr16:23,107,407
INFO	2016-11-02 07:41:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:27	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    2s.  Last read position: chr16:33,185,771
INFO	2016-11-02 07:41:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:29	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:08:03s.  Time for last 1,000,000:    1s.  Last read position: chr16:45,631,833
INFO	2016-11-02 07:41:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:33	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:08:07s.  Time for last 1,000,000:    4s.  Last read position: chr16:68,409,054
INFO	2016-11-02 07:41:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:36	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:08:09s.  Time for last 1,000,000:    2s.  Last read position: chr16:91,566,821
INFO	2016-11-02 07:41:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:38	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    2s.  Last read position: chr17:4,855,951
INFO	2016-11-02 07:41:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:40	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    2s.  Last read position: chr17:21,485,184
INFO	2016-11-02 07:41:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:43	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    2s.  Last read position: chr17:27,057,780
INFO	2016-11-02 07:41:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:45	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    1s.  Last read position: chr17:31,187,591
INFO	2016-11-02 07:41:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:47	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:08:21s.  Time for last 1,000,000:    2s.  Last read position: chr17:35,171,832
INFO	2016-11-02 07:41:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:49	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    2s.  Last read position: chr17:45,595,988
INFO	2016-11-02 07:41:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:51	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    1s.  Last read position: chr17:51,831,810
INFO	2016-11-02 07:41:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:53	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:08:26s.  Time for last 1,000,000:    1s.  Last read position: chr17:66,123,471
INFO	2016-11-02 07:41:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:55	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:    2s.  Last read position: chr17:79,638,904
INFO	2016-11-02 07:41:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:41:58	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    2s.  Last read position: chr17:87,592,599
INFO	2016-11-02 07:41:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:00	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    2s.  Last read position: chr18:15,065,350
INFO	2016-11-02 07:42:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:02	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    2s.  Last read position: chr18:35,178,171
INFO	2016-11-02 07:42:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:07	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    4s.  Last read position: chr18:48,087,177
INFO	2016-11-02 07:42:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:09	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    2s.  Last read position: chr18:61,916,281
INFO	2016-11-02 07:42:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:11	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    2s.  Last read position: chr18:74,709,802
INFO	2016-11-02 07:42:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:14	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    2s.  Last read position: chr18:83,722,728
INFO	2016-11-02 07:42:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:16	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    2s.  Last read position: chr19:6,077,181
INFO	2016-11-02 07:42:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:18	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    1s.  Last read position: chr19:15,202,459
INFO	2016-11-02 07:42:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:20	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    2s.  Last read position: chr19:32,227,077
INFO	2016-11-02 07:42:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:22	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,179,046
INFO	2016-11-02 07:42:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:24	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    2s.  Last read position: chr19:47,447,743
INFO	2016-11-02 07:42:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:26	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    2s.  Last read position: chr19:60,144,502
INFO	2016-11-02 07:42:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:28	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    1s.  Last read position: chrX:48,423,310
INFO	2016-11-02 07:42:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:31	MarkDuplicates	Read   202,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    2s.  Last read position: chrX:100,729,740
INFO	2016-11-02 07:42:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:33	MarkDuplicates	Read   203,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    2s.  Last read position: chrX:153,175,058
INFO	2016-11-02 07:42:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:42:34	MarkDuplicates	Read 203701093 records. 0 pairs never matched.
INFO	2016-11-02 07:42:37	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2369918864; totalMemory: 2456289280; maxMemory: 3817865216
INFO	2016-11-02 07:42:37	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 07:42:37	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 07:42:37	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 07:43:26	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 07:43:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3480793264; totalMemory: 3509059584; maxMemory: 3817865216
INFO	2016-11-02 07:43:29	MarkDuplicates	Marking 195124174 records as duplicates.
INFO	2016-11-02 07:43:29	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 07:44:30	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:01s.  Time for last 10,000,000:   61s.  Last read position: chr1:158,766,396
INFO	2016-11-02 07:45:39	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:10s.  Time for last 10,000,000:   68s.  Last read position: chr2:72,987,000
INFO	2016-11-02 07:46:53	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:03:24s.  Time for last 10,000,000:   73s.  Last read position: chr2:174,659,488
INFO	2016-11-02 07:47:53	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:04:24s.  Time for last 10,000,000:   60s.  Last read position: chr3:144,720,224
INFO	2016-11-02 07:48:53	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:05:24s.  Time for last 10,000,000:   60s.  Last read position: chr4:133,014,198
INFO	2016-11-02 07:49:54	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:06:25s.  Time for last 10,000,000:   60s.  Last read position: chr5:99,978,268
INFO	2016-11-02 07:50:57	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:07:28s.  Time for last 10,000,000:   62s.  Last read position: chr6:47,961,097
INFO	2016-11-02 07:52:02	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:08:33s.  Time for last 10,000,000:   65s.  Last read position: chr7:24,664,383
INFO	2016-11-02 07:53:11	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:09:42s.  Time for last 10,000,000:   69s.  Last read position: chr7:132,364,910
INFO	2016-11-02 07:54:20	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:10:51s.  Time for last 10,000,000:   68s.  Last read position: chr8:117,158,150
INFO	2016-11-02 07:55:20	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:11:51s.  Time for last 10,000,000:   60s.  Last read position: chr9:98,364,548
INFO	2016-11-02 07:56:21	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:12:52s.  Time for last 10,000,000:   60s.  Last read position: chr10:82,904,247
INFO	2016-11-02 07:57:21	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:13:52s.  Time for last 10,000,000:   60s.  Last read position: chr11:69,037,532
INFO	2016-11-02 07:58:22	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:14:53s.  Time for last 10,000,000:   60s.  Last read position: chr12:3,305,779
INFO	2016-11-02 07:59:22	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:15:53s.  Time for last 10,000,000:   60s.  Last read position: chr13:37,764,439
INFO	2016-11-02 08:00:23	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:16:54s.  Time for last 10,000,000:   60s.  Last read position: chr14:60,671,769
INFO	2016-11-02 08:01:24	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:17:55s.  Time for last 10,000,000:   61s.  Last read position: chr15:91,718,492
INFO	2016-11-02 08:02:24	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:18:55s.  Time for last 10,000,000:   60s.  Last read position: chr17:21,485,184
INFO	2016-11-02 08:03:25	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:19:56s.  Time for last 10,000,000:   60s.  Last read position: chr18:35,178,171
INFO	2016-11-02 08:04:26	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:20:57s.  Time for last 10,000,000:   61s.  Last read position: chr19:60,144,502
Could not delete file /tmp/imk1/sortingcollection.2676000097925011500.tmp
Could not delete file /tmp/imk1/sortingcollection.8586071198772256898.tmp
INFO	2016-11-02 08:04:49	MarkDuplicates	Before output close freeMemory: 2843171616; totalMemory: 2859466752; maxMemory: 3817865216
INFO	2016-11-02 08:04:50	MarkDuplicates	After output close freeMemory: 2843170800; totalMemory: 2859466752; maxMemory: 3817865216
[Wed Nov 02 08:04:50 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 31.42 minutes.
Runtime.totalMemory()=2859466752

 

 
# 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/SRR836459/out/align/rep1/SRR836459.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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/SRR836459/out/qc/rep1/SRR836459.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--------------------
13726 (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/SRR836459/out/align/rep1/SRR836459.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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--------------------
45938 (process ID) old priority 0, new priority 10

Waiting for 39 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/SRR836459/out/align/rep1/SRR836459.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.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--------------------
46062 (process ID) old priority 0, new priority 10
Waiting for 47 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/SRR836459/out/align/rep1/SRR836459.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/SRR836459/out/align/rep1/SRR836459.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/rep1/SRR836459.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr2/SRR836459.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/align/pseudo_reps/rep1/pr1/SRR836459.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--------------------
46063 (process ID) old priority 0, new priority 10
Waiting for 42 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/SRR836459/out/align/rep1/SRR836459.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/out/qc/rep1/SRR836459.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--------------------
14607 (process ID) old priority 0, new priority 10

  
--------------------Post mortem info--------------------
==============================================================
job_number:                 3323
exec_file:                  job_scripts/3323
submission_time:            Wed Nov  2 08:27:42 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/SRR836459
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836459/chipseq.bds.20161101_222023_216_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/SRR836459/chipseq.bds.20161101_222023_216_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=34563.SRR836459.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/SRR836459,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