xcor rep1

 chipseq.bds.20161101_222023_947_parallel_43/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20161101_222023_947_parallel_43/task.align_bwa.bwa_sam_ctl1.line_140.id_13
chipseq.bds.20161101_222023_947_parallel_43/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20161101_222023_947_parallel_43/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15
chipseq.bds.20161101_222023_947_parallel_43/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20161101_222023_947_parallel_43/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17
 

 chipseq.bds.20161101_222023_947_parallel_42/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20161101_222023_947_parallel_42/task.align_bwa.bwa_sam_rep1.line_140.id_12
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20161101_222023_947_parallel_42/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20161101_222023_947_parallel_42/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/SRR836477.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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--------------------
45984 (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] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.86 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.24 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 14.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.71 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 8.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.22 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.54 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.58 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.11 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.83 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.38 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.48 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.74 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.71 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.07 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.68 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.66 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.66 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.53 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.74 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.68 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.72 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.92 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.72 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.64 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.49 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.69 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.56 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.60 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.67 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.65 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.87 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 3.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.87 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.97 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.93 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.96 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.76 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.68 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.87 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.88 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.92 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.02 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.87 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.01 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.96 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.05 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.02 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 1.66 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.00 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.00 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.42 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 15.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 17.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 16.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 6.76 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 150043467 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/SRR836477.fastq.gz
[main] Real time: 11925.965 sec; CPU: 45032.712 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/SRR836477/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--------------------
21930 (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... 41.72 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... 41.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1310720 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... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.55 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... 40.95 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... 40.77 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... 41.71 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... 43.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.40 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... 48.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.73 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... 42.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% 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] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.53 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... 40.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.95 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... 43.52 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.20 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... 41.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.16 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... 41.66 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... 41.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.02 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... 41.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.36 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... 48.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.64 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... 53.22 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.63 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... 45.78 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... 42.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.19 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... 44.36 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... 44.21 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... 44.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.15 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... 40.89 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.93 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... 40.91 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.01 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.43 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... 41.10 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... 40.82 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... 42.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.08 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... 50.59 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... 45.99 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... 44.66 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... 42.63 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.28 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.10 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... 41.54 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... 39.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.17 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... 41.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.53 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.44 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... 41.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.18 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.89 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... 44.72 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... 47.15 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... 47.39 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... 46.04 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... 43.07 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... 40.88 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... 40.20 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.72 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 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... 40.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.50 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... 41.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 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... 43.04 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... 47.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.23 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.28 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... 40.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.89 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... 43.06 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... 41.31 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.36 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.86 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... 41.06 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... 40.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.76 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.85 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.93 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... 42.15 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... 42.88 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... 43.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.00 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: 5344.236 sec; CPU: 5343.232 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/SRR836477/out/align/rep1/SRR836477.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836477.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.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--------------------
9668 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 2.6% 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... [samopen] SAM header is present: 96 sequences.
0.28 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.43 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.26 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.52 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.11 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.60 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.72 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.76 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.73 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.85 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.34 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.20 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.51 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.99 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.65 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.36 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 3.4% 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... 0.24 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.25 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.19 sec
[bwa_aln_core] refine gapped alignments... 1.20 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.94 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 6.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.24 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.90 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.48 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.00 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.64 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.43 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.52 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 2.65 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.95 sec
[bwa_aln_core] refine gapped alignments... 1.96 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.02 sec
[bwa_aln_core] refine gapped alignments... 6.15 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.22 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.61 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.66 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.99 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.73 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.72 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.63 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.70 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.06 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.19 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.71 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.33 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 3.2% 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... 0.41 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.20 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.62 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.76 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.90 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.39 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.8% 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] 27525120 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.68 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.37 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.96 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.92 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.51 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.22 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.08 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.86 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.79 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.69 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.89 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.50 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.70 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.59 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.08 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.04 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.93 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.16 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.75 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.02 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.10 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.11 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.41 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.62 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.66 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 5.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.97 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.64 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.66 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.95 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.70 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.15 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.08 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.56 sec
[bwa_aln_core] refine gapped alignments... 5.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.66 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.89 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.63 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.85 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.63 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.66 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.36 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.68 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.11 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.06 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.68 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.29 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.79 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.80 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.26 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.98 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.22 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.90 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.54 sec
[bwa_aln_core] refine gapped alignments... 3.82 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.21 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.34 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.39 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.69 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.76 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.52 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.54 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.94 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.78 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.27 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.90 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.53 sec
[bwa_aln_core] refine gapped alignments... 5.83 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.93 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.24 sec
[bwa_aln_core] refine gapped alignments... 3.18 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.63 sec
[bwa_aln_core] refine gapped alignments... 8.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.37 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.23 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.18 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 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] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.64 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.92 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.7% 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... 0.25 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.98 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.89 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.95 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.04 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.95 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.59 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.64 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.65 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.43 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.74 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.67 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.08 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.28 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.04 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.10 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.18 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.13 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.94 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.17 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.13 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.16 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.41 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.65 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.59 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.18 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.17 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.16 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.17 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.16 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.12 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.21 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.17 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.20 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.97 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.97 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.81 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.79 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.83 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.76 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.10 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.10 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.76 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.83 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.81 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.17 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.83 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.77 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.14 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.80 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.12 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.16 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.82 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.86 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.15 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 4.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.18 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.19 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.22 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.23 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.00 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.15 sec
[bwa_aln_core] 150043467 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/SRR836477/out/align/rep1/SRR836477.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836477.fastq.gz
[main] Real time: 5489.834 sec; CPU: 5198.384 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/SRR836477/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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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--------------------
1349 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.47 sec
[bwa_aln_core] 262144 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... 0.58 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.45 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... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1572864 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... 0.53 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 6.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.47 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... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.69 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.65 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.68 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.71 sec
[bwa_aln_core] refine gapped alignments... 0.34 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... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 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... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 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... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 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... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.67 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.98 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.09 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/SRR836477/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: 680.052 sec; CPU: 526.388 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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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--------------------
24030 (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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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--------------------
24450 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 02:37:10 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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 02:37:10 PDT 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 02:37:10	MarkDuplicates	Start of doWork freeMemory: 254881776; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 02:37:10	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 02:37:10	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 02:37:17	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    5s.  Last read position: chr1:169,651,309
INFO	2016-11-02 02:37:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:20	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr2:120,600,340
INFO	2016-11-02 02:37:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:25	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    4s.  Last read position: chr3:96,659,413
INFO	2016-11-02 02:37:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:29	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    4s.  Last read position: chr4:108,195,091
INFO	2016-11-02 02:37:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:32	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr5:103,594,339
INFO	2016-11-02 02:37:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:36	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    4s.  Last read position: chr6:98,592,333
INFO	2016-11-02 02:37:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:39	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr7:114,109,505
INFO	2016-11-02 02:37:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:43	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr8:121,515,352
INFO	2016-11-02 02:37:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:45	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    2s.  Last read position: chr10:14,536,964
INFO	2016-11-02 02:37:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:48	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    3s.  Last read position: chr11:32,924,585
INFO	2016-11-02 02:37:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:51	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr12:41,050,039
INFO	2016-11-02 02:37:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:55	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    4s.  Last read position: chr13:80,878,598
INFO	2016-11-02 02:37:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:37:58	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr15:12,027,335
INFO	2016-11-02 02:37:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:01	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    3s.  Last read position: chr16:56,024,589
INFO	2016-11-02 02:38:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:14	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:   13s.  Last read position: chr18:10,030,498
INFO	2016-11-02 02:38:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:18	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    3s.  Last read position: chrX:36,565,109
INFO	2016-11-02 02:38:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 02:38:19	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 02:38:20	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1705497312; totalMemory: 1792016384; maxMemory: 3817865216
INFO	2016-11-02 02:38:20	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 02:38:20	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 02:38:20	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 02:38:25	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 02:38:25	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1819078120; totalMemory: 2800746496; maxMemory: 3817865216
INFO	2016-11-02 02:38:25	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 02:38:25	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 02:39:42	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:16s.  Time for last 10,000,000:   76s.  Last read position: chr11:32,924,585
INFO	2016-11-02 02:40:34	MarkDuplicates	Before output close freeMemory: 2786285576; totalMemory: 2815426560; maxMemory: 3817865216
INFO	2016-11-02 02:40:34	MarkDuplicates	After output close freeMemory: 2805158888; totalMemory: 2834300928; maxMemory: 3817865216
[Wed Nov 02 02:40:34 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.41 minutes.
Runtime.totalMemory()=2834300928

 

 
# 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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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/SRR836477/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/SRR836477/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/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/SRR836477/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/SRR836477/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--------------------
30080 (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/SRR836477/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/SRR836477/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--------------------
30198 (process ID) old priority 0, new priority 10

Waiting for 51 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/SRR836477/out/align/rep1/SRR836477.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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/SRR836477/out/align/rep1/SRR836477.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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--------------------
13544 (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/SRR836477/out/align/rep1/SRR836477.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.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--------------------
9818 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 07:52:55 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.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 07:52:55 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 07:52:56	MarkDuplicates	Start of doWork freeMemory: 254882272; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 07:52:56	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 07:52:56	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 07:52:58	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836477.7678607'.  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 07:53:08	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr1:62,176,347
INFO	2016-11-02 07:53:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:53:48	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:   40s.  Last read position: chr1:123,210,967
INFO	2016-11-02 07:53:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:01	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:   12s.  Last read position: chr1:171,175,376
INFO	2016-11-02 07:54:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:05	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    4s.  Last read position: chr2:32,177,912
INFO	2016-11-02 07:54:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:17	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:   11s.  Last read position: chr2:80,109,481
INFO	2016-11-02 07:54:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:25	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    7s.  Last read position: chr2:130,087,689
INFO	2016-11-02 07:54:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:36	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:   11s.  Last read position: chr3:12,992,475
INFO	2016-11-02 07:54:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:41	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    4s.  Last read position: chr3:73,029,438
INFO	2016-11-02 07:54:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:46	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    5s.  Last read position: chr3:123,322,285
INFO	2016-11-02 07:54:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:50	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:52s.  Time for last 1,000,000:    3s.  Last read position: chr4:19,960,248
INFO	2016-11-02 07:54:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:54:54	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    3s.  Last read position: chr4:81,950,634
INFO	2016-11-02 07:54:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:02	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    7s.  Last read position: chr4:136,278,201
INFO	2016-11-02 07:55:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:07	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    5s.  Last read position: chr5:45,655,001
INFO	2016-11-02 07:55:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:12	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    5s.  Last read position: chr5:103,720,535
INFO	2016-11-02 07:55:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:33	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:02:35s.  Time for last 1,000,000:   21s.  Last read position: chr6:13,099,692
INFO	2016-11-02 07:55:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:37	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:02:39s.  Time for last 1,000,000:    3s.  Last read position: chr6:69,071,541
INFO	2016-11-02 07:55:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:42	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    5s.  Last read position: chr6:128,406,327
INFO	2016-11-02 07:55:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:46	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:02:48s.  Time for last 1,000,000:    4s.  Last read position: chr7:55,443,066
INFO	2016-11-02 07:55:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:51	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    4s.  Last read position: chr7:112,629,862
INFO	2016-11-02 07:55:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:55:55	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    4s.  Last read position: chr8:34,744,525
INFO	2016-11-02 07:55:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:00	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    5s.  Last read position: chr8:93,503,954
INFO	2016-11-02 07:56:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:05	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    4s.  Last read position: chr9:28,317,029
INFO	2016-11-02 07:56:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:08	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chr9:82,018,850
INFO	2016-11-02 07:56:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:12	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    4s.  Last read position: chr10:17,121,589
INFO	2016-11-02 07:56:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:16	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    3s.  Last read position: chr10:69,170,612
INFO	2016-11-02 07:56:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:21	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:03:23s.  Time for last 1,000,000:    5s.  Last read position: chr10:120,985,062
INFO	2016-11-02 07:56:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:24	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:03:26s.  Time for last 1,000,000:    2s.  Last read position: chr11:49,244,804
INFO	2016-11-02 07:56:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:27	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    2s.  Last read position: chr11:99,129,966
INFO	2016-11-02 07:56:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:31	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chr12:40,760,210
INFO	2016-11-02 07:56:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:42	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:   11s.  Last read position: chr12:96,950,068
INFO	2016-11-02 07:56:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:46	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:03:47s.  Time for last 1,000,000:    3s.  Last read position: chr13:37,868,818
INFO	2016-11-02 07:56:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:49	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:03:51s.  Time for last 1,000,000:    3s.  Last read position: chr13:95,566,715
INFO	2016-11-02 07:56:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:52	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    3s.  Last read position: chr14:40,429,965
INFO	2016-11-02 07:56:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:56	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    3s.  Last read position: chr14:99,037,226
INFO	2016-11-02 07:56:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:56:59	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    3s.  Last read position: chr15:38,206,343
INFO	2016-11-02 07:56:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:02	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    2s.  Last read position: chr15:97,293,095
INFO	2016-11-02 07:57:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:05	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:    2s.  Last read position: chr16:49,171,577
INFO	2016-11-02 07:57:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:09	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:    4s.  Last read position: chr17:7,249,725
INFO	2016-11-02 07:57:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:12	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    2s.  Last read position: chr17:63,277,492
INFO	2016-11-02 07:57:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:17	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    4s.  Last read position: chr18:32,222,185
INFO	2016-11-02 07:57:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:21	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    4s.  Last read position: chr18:87,341,964
INFO	2016-11-02 07:57:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:25	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    3s.  Last read position: chr19:53,375,634
INFO	2016-11-02 07:57:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:29	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:04:30s.  Time for last 1,000,000:    3s.  Last read position: chrX:117,641,954
INFO	2016-11-02 07:57:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 07:57:34	MarkDuplicates	Read 43535249 records. 0 pairs never matched.
INFO	2016-11-02 07:57:39	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2693347088; totalMemory: 2779774976; maxMemory: 3817865216
INFO	2016-11-02 07:57:39	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 07:57:39	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 07:57:39	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 07:57:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 07:57:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2097777760; totalMemory: 3079143424; maxMemory: 3817865216
INFO	2016-11-02 07:57:59	MarkDuplicates	Marking 20402092 records as duplicates.
INFO	2016-11-02 07:57:59	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 07:59:49	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:50s.  Time for last 10,000,000:  110s.  Last read position: chr4:19,960,248
INFO	2016-11-02 08:02:12	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:04:13s.  Time for last 10,000,000:  143s.  Last read position: chr8:34,744,525
INFO	2016-11-02 08:04:31	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:06:32s.  Time for last 10,000,000:  138s.  Last read position: chr12:96,950,068
INFO	2016-11-02 08:06:12	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:08:13s.  Time for last 10,000,000:  101s.  Last read position: chr18:32,222,185
INFO	2016-11-02 08:07:00	MarkDuplicates	Before output close freeMemory: 3100100392; totalMemory: 3129999360; maxMemory: 3817865216
INFO	2016-11-02 08:07:01	MarkDuplicates	After output close freeMemory: 3100099336; totalMemory: 3129999360; maxMemory: 3817865216
[Wed Nov 02 08:07:01 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 14.10 minutes.
Runtime.totalMemory()=3129999360

 

 
# 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/SRR836477/out/align/rep1/SRR836477.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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/SRR836477/out/qc/rep1/SRR836477.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--------------------
44342 (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/SRR836477/out/align/rep1/SRR836477.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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--------------------
45241 (process ID) old priority 0, new priority 10

Waiting for 2 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/SRR836477/out/align/rep1/SRR836477.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.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--------------------
45510 (process ID) old priority 0, new priority 10
Waiting for 33 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/SRR836477/out/align/rep1/SRR836477.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/SRR836477/out/align/rep1/SRR836477.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/rep1/SRR836477.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr2/SRR836477.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/align/pseudo_reps/rep1/pr1/SRR836477.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--------------------
45505 (process ID) old priority 0, new priority 10
Waiting for 8 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/SRR836477/out/align/rep1/SRR836477.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/out/qc/rep1/SRR836477.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--------------------
14243 (process ID) old priority 0, new priority 10

  
--------------------Post mortem info--------------------
==============================================================
job_number:                 3318
submission_time:            Wed Nov  2 08:17:26 2016
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_path:                 /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836477/chipseq.bds.20161101_222023_947_parallel_42/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/SRR836477/chipseq.bds.20161101_222023_947_parallel_42/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=36024.SRR836477.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/SRR836477,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
parallel environment:  shm range: 4
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