xcor rep1

 chipseq.bds.20161101_222025_262_parallel_43/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20161101_222025_262_parallel_43/task.align_bwa.bwa_sam_ctl1.line_140.id_13
chipseq.bds.20161101_222025_262_parallel_43/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20161101_222025_262_parallel_43/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15
chipseq.bds.20161101_222025_262_parallel_43/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20161101_222025_262_parallel_43/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17
 

 chipseq.bds.20161101_222025_262_parallel_42/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20161101_222025_262_parallel_42/task.align_bwa.bwa_sam_rep1.line_140.id_12
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20161101_222025_262_parallel_42/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20161101_222025_262_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/SRR836483.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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--------------------
24985 (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] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.42 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.13 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.42 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% 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] 88080384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.13 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.17 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.25 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.94 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.55 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.11 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.47 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.83 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.25 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.7% 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] 164888576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 12.73 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 180969309 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/SRR836483.fastq.gz
[main] Real time: 9823.842 sec; CPU: 36819.660 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/SRR836483/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--------------------
26534 (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... 53.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.50 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... 52.78 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... 53.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.60 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... 53.92 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... 52.43 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... 63.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.61 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... 60.45 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... 59.67 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... 58.28 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... 56.69 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... 52.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.10 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... 55.74 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... 57.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.60 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... 53.46 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... 56.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.22 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... 56.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.24 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.23 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... 58.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.32 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... 66.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.90 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... 59.03 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... 55.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.93 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.32 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... 56.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.41 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... 53.13 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... 52.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.78 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... 53.59 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... 52.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.74 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... 52.84 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... 50.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.85 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... 63.19 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... 58.41 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... 55.64 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... 52.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.38 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... 55.79 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... 52.68 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... 47.33 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.86 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.64 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... 52.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.77 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... 53.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.65 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... 54.85 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... 51.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.03 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... 57.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.07 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... 61.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.11 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... 51.36 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... 50.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.79 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... 52.63 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... 52.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.32 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... 53.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.65 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... 54.79 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... 54.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.66 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... 59.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.15 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... 68.16 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... 68.31 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.94 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... 54.14 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... 52.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.19 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... 51.03 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... 52.79 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% 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] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.56 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... 49.36 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... 50.15 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.34 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... 50.52 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... 49.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.43 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... 52.88 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.37 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... 52.79 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.54 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.50 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... 50.78 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... 50.10 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... 51.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.77 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: 6738.777 sec; CPU: 6738.664 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/SRR836483/out/align/rep1/SRR836483.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836483.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.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--------------------
6288 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.23 sec
[bwa_aln_core] refine gapped alignments... 2.93 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.46 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.56 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.75 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.38 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.78 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.16 sec
[bwa_aln_core] refine gapped alignments... 2.07 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.65 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.90 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.81 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.09 sec
[bwa_aln_core] refine gapped alignments... 1.21 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.03 sec
[bwa_aln_core] refine gapped alignments... 1.29 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.00 sec
[bwa_aln_core] refine gapped alignments... 1.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.00 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.47 sec
[bwa_aln_core] refine gapped alignments... 1.96 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.20 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.55 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.03 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.03 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.28 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.44 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.65 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.78 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.40 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 2.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.78 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.54 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.53 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.94 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.01 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.17 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.03 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.93 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.89 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.65 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.55 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.96 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.58 sec
[bwa_aln_core] refine gapped alignments... 3.27 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.84 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.16 sec
[bwa_aln_core] refine gapped alignments... 2.05 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.16 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.54 sec
[bwa_aln_core] refine gapped alignments... 3.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.24 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.97 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.60 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.22 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.24 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.89 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.33 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.67 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 1.94 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.23 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.16 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.22 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.17 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.87 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.21 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.97 sec
[bwa_aln_core] refine gapped alignments... 3.35 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.51 sec
[bwa_aln_core] refine gapped alignments... 3.13 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.05 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.19 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.18 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.13 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.53 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.44 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.06 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.73 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.45 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.67 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.56 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.91 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.34 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.67 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.92 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.80 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.02 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.77 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.12 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.07 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.03 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.40 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.73 sec
[bwa_aln_core] refine gapped alignments... 1.54 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.51 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.37 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.70 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.69 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.54 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.41 sec
[bwa_aln_core] refine gapped alignments... 0.98 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.86 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.91 sec
[bwa_aln_core] refine gapped alignments... 1.29 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.20 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.42 sec
[bwa_aln_core] refine gapped alignments... 1.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.72 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.41 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.57 sec
[bwa_aln_core] refine gapped alignments... 1.95 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.63 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.28 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 1.66 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.26 sec
[bwa_aln_core] refine gapped alignments... 1.87 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.47 sec
[bwa_aln_core] refine gapped alignments... 1.92 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.30 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.09 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.00 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.16 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.55 sec
[bwa_aln_core] refine gapped alignments... 2.36 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.24 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.33 sec
[bwa_aln_core] refine gapped alignments... 2.11 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.39 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.17 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.77 sec
[bwa_aln_core] refine gapped alignments... 1.67 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.69 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.84 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.56 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.64 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.09 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.92 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.29 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.00 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.89 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.11 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.56 sec
[bwa_aln_core] refine gapped alignments... 1.63 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.68 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.39 sec
[bwa_aln_core] refine gapped alignments... 2.31 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.53 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.97 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.47 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.88 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.47 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 64487424 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... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.51 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.70 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 66584576 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... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.23 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.06 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.50 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.74 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.26 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.16 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.80 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.81 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.22 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.50 sec
[bwa_aln_core] refine gapped alignments... 2.82 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.53 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.20 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.88 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.58 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.45 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.07 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.22 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.60 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.57 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.32 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.40 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.74 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.38 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.87 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.25 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.05 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.69 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.71 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.55 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.93 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.18 sec
[bwa_aln_core] refine gapped alignments... 1.28 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.97 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.99 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.01 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.34 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.61 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.01 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.23 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.06 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.43 sec
[bwa_aln_core] refine gapped alignments... 1.08 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.64 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.29 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.59 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.33 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.02 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.08 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.81 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.01 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.77 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 2.19 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.18 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.18 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.08 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.52 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.88 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.79 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.28 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.97 sec
[bwa_aln_core] refine gapped alignments... 1.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.39 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.93 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.24 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.47 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.03 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.62 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.54 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.34 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.72 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.36 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.48 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.64 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 109576192 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... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.1% 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... 0.38 sec
[bwa_aln_core] 111411200 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... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.67 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.37 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% 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... 0.50 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.51 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 115081216 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... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.40 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.37 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 2.25 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 1.28 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 1.26 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 2.13 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.85 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.46 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.64 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.68 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.75 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.80 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.33 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.48 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.70 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 134479872 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... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.4% 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... 0.35 sec
[bwa_aln_core] 135790592 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... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.68 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.41 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 2.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.80 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.11 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.29 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.96 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.83 sec
[bwa_aln_core] refine gapped alignments... 2.66 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.68 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.58 sec
[bwa_aln_core] refine gapped alignments... 2.02 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.16 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 4.4% 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... 0.37 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.71 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.22 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.32 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.73 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.64 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.61 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.57 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.75 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 151781376 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... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.37 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.3% 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... 0.44 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.89 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.66 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 3.3% 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... 0.39 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.9% 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... 0.39 sec
[bwa_aln_core] 154664960 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... 0.46 sec
[bwa_aln_core] 154927104 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... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 155189248 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... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.74 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.6% 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... 0.45 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.3% 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... 0.35 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.00 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.69 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.35 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.95 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 161480704 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... 0.35 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.4% 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... 0.38 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.7% 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... 0.34 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.65 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.7% 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... 0.41 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 2.2% 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... 0.45 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.01 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.70 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.54 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.52 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 169345024 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... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 3.11 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.37 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.97 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 175112192 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... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.36 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.83 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.71 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.72 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.71 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.3% 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... 0.55 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.3% 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... 0.46 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.29 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 180969309 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/SRR836483/out/align/rep1/SRR836483.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836483.fastq.gz
[main] Real time: 6976.366 sec; CPU: 6530.284 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/SRR836483/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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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--------------------
24127 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.30 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.74 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.57 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.05 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.82 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.65 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.21 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.92 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 10.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.42 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 12.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.58 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 12.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.52 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 11.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.75 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.95 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 4.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.42 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.47 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.63 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.79 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.46 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.55 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.65 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.75 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.99 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 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... 11.88 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.08 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 13.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.03 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 13.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.88 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.75 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 11.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 9.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 6.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.50 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 5.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.16 sec
[bwa_aln_core] refine gapped alignments... 1.33 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 3.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.29 sec
[bwa_aln_core] refine gapped alignments... 1.14 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.57 sec
[bwa_aln_core] refine gapped alignments... 1.78 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.64 sec
[bwa_aln_core] refine gapped alignments... 1.87 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... 12.62 sec
[bwa_aln_core] refine gapped alignments... 1.72 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.34 sec
[bwa_aln_core] refine gapped alignments... 1.79 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.49 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.76 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.79 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 4.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.60 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 8.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 11.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.79 sec
[bwa_aln_core] refine gapped alignments... 1.18 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.26 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.70 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 10.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.11 sec
[bwa_aln_core] refine gapped alignments... 1.59 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 8.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.62 sec
[bwa_aln_core] refine gapped alignments... 1.95 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 6.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.09 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 4.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.69 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.90 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.14 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.05 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.23 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.89 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.63 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.86 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 4.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.90 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 9.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.94 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 12.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.98 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 12.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 0.77 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.07 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 9.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.08 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.84 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 5.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.87 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.28 sec
[bwa_aln_core] refine gapped alignments... 0.69 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.98 sec
[bwa_aln_core] refine gapped alignments... 0.74 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.98 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.5% 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... 0.35 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.16 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.18 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.96 sec
[bwa_aln_core] refine gapped alignments... 0.72 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.84 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.90 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.97 sec
[bwa_aln_core] refine gapped alignments... 1.04 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 6.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.61 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.00 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 14.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.76 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 13.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.77 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 11.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.86 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 9.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.77 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.51 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.65 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.19 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.68 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.50 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.12 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.46 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 5.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.83 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.96 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 12.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.42 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 12.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.10 sec
[bwa_aln_core] refine gapped alignments... 2.95 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 11.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.78 sec
[bwa_aln_core] refine gapped alignments... 2.53 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 9.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.90 sec
[bwa_aln_core] refine gapped alignments... 2.97 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 7.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.73 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 5.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.96 sec
[bwa_aln_core] refine gapped alignments... 3.06 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.18 sec
[bwa_aln_core] refine gapped alignments... 2.74 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.23 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.39 sec
[bwa_aln_core] refine gapped alignments... 3.17 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.46 sec
[bwa_aln_core] refine gapped alignments... 2.99 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.79 sec
[bwa_aln_core] refine gapped alignments... 3.02 sec
[bwa_aln_core] print alignments... 0.10 sec
[bwa_aln_core] 32022635 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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: 1970.829 sec; CPU: 1833.040 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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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--------------------
15689 (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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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--------------------
26991 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 03:23:09 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 02 03:23:09 PDT 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 03:23:09	MarkDuplicates	Start of doWork freeMemory: 254881632; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 03:23:09	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 03:23:09	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-02 03:23:14	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 03:23:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:18	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    3s.  Last read position: chr2:120,600,340
INFO	2016-11-02 03:23:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:22	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    3s.  Last read position: chr3:96,659,413
INFO	2016-11-02 03:23:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:25	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:15s.  Time for last 1,000,000:    3s.  Last read position: chr4:108,195,091
INFO	2016-11-02 03:23:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:28	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    3s.  Last read position: chr5:103,594,339
INFO	2016-11-02 03:23:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:32	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:22s.  Time for last 1,000,000:    3s.  Last read position: chr6:98,592,333
INFO	2016-11-02 03:23:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:35	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    2s.  Last read position: chr7:114,109,505
INFO	2016-11-02 03:23:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:37	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr8:121,515,352
INFO	2016-11-02 03:23:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:41	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    3s.  Last read position: chr10:14,536,964
INFO	2016-11-02 03:23:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:44	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    2s.  Last read position: chr11:32,924,585
INFO	2016-11-02 03:23:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:47	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    2s.  Last read position: chr12:41,050,039
INFO	2016-11-02 03:23:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:51	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr13:80,878,598
INFO	2016-11-02 03:23:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:54	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:44s.  Time for last 1,000,000:    2s.  Last read position: chr15:12,027,335
INFO	2016-11-02 03:23:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:23:56	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    2s.  Last read position: chr16:56,024,589
INFO	2016-11-02 03:23:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:24:10	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:   14s.  Last read position: chr18:10,030,498
INFO	2016-11-02 03:24:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:24:13	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    2s.  Last read position: chrX:36,565,109
INFO	2016-11-02 03:24:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 03:24:15	MarkDuplicates	Read 16572675 records. 0 pairs never matched.
INFO	2016-11-02 03:24:15	MarkDuplicates	After buildSortedReadEndLists freeMemory: 1737624664; totalMemory: 1823997952; maxMemory: 3817865216
INFO	2016-11-02 03:24:15	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 03:24:15	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 03:24:15	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 03:24:22	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 03:24:22	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1856365040; totalMemory: 2837970944; maxMemory: 3817865216
INFO	2016-11-02 03:24:22	MarkDuplicates	Marking 13188493 records as duplicates.
INFO	2016-11-02 03:24:22	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 03:25:38	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 03:26:31	MarkDuplicates	Before output close freeMemory: 2828182328; totalMemory: 2857369600; maxMemory: 3817865216
INFO	2016-11-02 03:26:32	MarkDuplicates	After output close freeMemory: 2847055640; totalMemory: 2876243968; maxMemory: 3817865216
[Wed Nov 02 03:26:32 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.38 minutes.
Runtime.totalMemory()=2876243968

 

 
# 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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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/SRR836483/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/SRR836483/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/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/SRR836483/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/SRR836483/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--------------------
27398 (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/SRR836483/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/SRR836483/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--------------------
27622 (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/SRR836483/out/align/rep1/SRR836483.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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/SRR836483/out/align/rep1/SRR836483.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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--------------------
11453 (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/SRR836483/out/align/rep1/SRR836483.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.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--------------------
10998 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 02 08:27:12 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 02 08:27:12 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-02 08:27:12	MarkDuplicates	Start of doWork freeMemory: 254882792; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-02 08:27:12	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-02 08:27:12	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
WARNING	2016-11-02 08:27:12	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836483.14409346'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2016-11-02 08:27:20	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:29,517,405
INFO	2016-11-02 08:27:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:25	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    4s.  Last read position: chr1:46,670,583
INFO	2016-11-02 08:27:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:29	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    4s.  Last read position: chr1:64,719,783
INFO	2016-11-02 08:27:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:34	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    4s.  Last read position: chr1:84,114,666
INFO	2016-11-02 08:27:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:39	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    4s.  Last read position: chr1:98,100,150
INFO	2016-11-02 08:27:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:44	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    5s.  Last read position: chr1:125,560,737
INFO	2016-11-02 08:27:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:49	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    4s.  Last read position: chr1:136,831,409
INFO	2016-11-02 08:27:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:27:55	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:42s.  Time for last 1,000,000:    6s.  Last read position: chr1:156,018,957
INFO	2016-11-02 08:27:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:01	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    6s.  Last read position: chr1:170,583,789
INFO	2016-11-02 08:28:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:07	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    5s.  Last read position: chr1:182,254,747
INFO	2016-11-02 08:28:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:10	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    3s.  Last read position: chr2:3,788,264
INFO	2016-11-02 08:28:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:15	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    4s.  Last read position: chr2:22,729,359
INFO	2016-11-02 08:28:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:20	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    4s.  Last read position: chr2:31,472,506
INFO	2016-11-02 08:28:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:24	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    4s.  Last read position: chr2:45,104,763
INFO	2016-11-02 08:28:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:45	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:   21s.  Last read position: chr2:65,550,167
INFO	2016-11-02 08:28:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:49	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    3s.  Last read position: chr2:80,599,666
INFO	2016-11-02 08:28:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:53	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:40s.  Time for last 1,000,000:    4s.  Last read position: chr2:98,666,824
INFO	2016-11-02 08:28:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:28:58	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    4s.  Last read position: chr2:109,454,577
INFO	2016-11-02 08:28:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:04	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    5s.  Last read position: chr2:124,584,241
INFO	2016-11-02 08:29:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:07	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    3s.  Last read position: chr2:137,330,271
INFO	2016-11-02 08:29:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:10	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    3s.  Last read position: chr2:153,795,500
INFO	2016-11-02 08:29:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:14	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr2:164,745,940
INFO	2016-11-02 08:29:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:18	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    3s.  Last read position: chr2:173,781,864
INFO	2016-11-02 08:29:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:21	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    3s.  Last read position: chr3:19,128,726
INFO	2016-11-02 08:29:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:25	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    4s.  Last read position: chr3:41,162,732
INFO	2016-11-02 08:29:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:30	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    5s.  Last read position: chr3:63,929,102
INFO	2016-11-02 08:29:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:35	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    4s.  Last read position: chr3:85,569,086
INFO	2016-11-02 08:29:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:39	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    4s.  Last read position: chr3:96,122,887
INFO	2016-11-02 08:29:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:29:43	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    3s.  Last read position: chr3:108,134,512
INFO	2016-11-02 08:29:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:00	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:   16s.  Last read position: chr3:127,621,534
INFO	2016-11-02 08:30:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:04	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    3s.  Last read position: chr3:144,053,841
INFO	2016-11-02 08:30:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:07	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:54s.  Time for last 1,000,000:    3s.  Last read position: chr4:6,990,979
INFO	2016-11-02 08:30:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:10	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:    3s.  Last read position: chr4:32,389,012
INFO	2016-11-02 08:30:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:13	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:03:01s.  Time for last 1,000,000:    3s.  Last read position: chr4:46,946,173
INFO	2016-11-02 08:30:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:16	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:03s.  Time for last 1,000,000:    2s.  Last read position: chr4:64,833,925
INFO	2016-11-02 08:30:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:19	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    3s.  Last read position: chr4:93,096,409
INFO	2016-11-02 08:30:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:22	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:10s.  Time for last 1,000,000:    3s.  Last read position: chr4:109,106,080
INFO	2016-11-02 08:30:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:27	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    4s.  Last read position: chr4:123,519,094
INFO	2016-11-02 08:30:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:33	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    6s.  Last read position: chr4:133,007,535
INFO	2016-11-02 08:30:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:37	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:25s.  Time for last 1,000,000:    4s.  Last read position: chr4:140,257,389
INFO	2016-11-02 08:30:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:41	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:29s.  Time for last 1,000,000:    4s.  Last read position: chr4:152,131,133
INFO	2016-11-02 08:30:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:45	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:32s.  Time for last 1,000,000:    3s.  Last read position: chr5:20,851,410
INFO	2016-11-02 08:30:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:50	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:37s.  Time for last 1,000,000:    4s.  Last read position: chr5:33,683,327
INFO	2016-11-02 08:30:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:30:56	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    6s.  Last read position: chr5:52,499,319
INFO	2016-11-02 08:30:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:05	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    8s.  Last read position: chr5:73,065,551
INFO	2016-11-02 08:31:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:09	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:57s.  Time for last 1,000,000:    4s.  Last read position: chr5:96,777,186
INFO	2016-11-02 08:31:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:13	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    3s.  Last read position: chr5:110,638,211
INFO	2016-11-02 08:31:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:17	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:04:05s.  Time for last 1,000,000:    4s.  Last read position: chr5:120,618,005
INFO	2016-11-02 08:31:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:21	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:    3s.  Last read position: chr5:130,120,325
INFO	2016-11-02 08:31:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:25	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    3s.  Last read position: chr5:140,701,524
INFO	2016-11-02 08:31:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:29	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:16s.  Time for last 1,000,000:    4s.  Last read position: chr5:151,212,276
INFO	2016-11-02 08:31:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:34	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    4s.  Last read position: chr6:29,046,729
INFO	2016-11-02 08:31:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:37	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    3s.  Last read position: chr6:44,979,465
INFO	2016-11-02 08:31:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:41	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:28s.  Time for last 1,000,000:    3s.  Last read position: chr6:61,542,641
INFO	2016-11-02 08:31:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:45	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:    3s.  Last read position: chr6:83,795,854
INFO	2016-11-02 08:31:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:49	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    3s.  Last read position: chr6:97,068,477
INFO	2016-11-02 08:31:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:52	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:39s.  Time for last 1,000,000:    3s.  Last read position: chr6:114,663,210
INFO	2016-11-02 08:31:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:31:55	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    3s.  Last read position: chr6:126,478,115
INFO	2016-11-02 08:31:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:03	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    8s.  Last read position: chr6:143,094,782
INFO	2016-11-02 08:32:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:07	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    3s.  Last read position: chr7:16,358,951
INFO	2016-11-02 08:32:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:10	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    3s.  Last read position: chr7:29,482,440
INFO	2016-11-02 08:32:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:14	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    3s.  Last read position: chr7:45,528,225
INFO	2016-11-02 08:32:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:17	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    3s.  Last read position: chr7:67,372,679
INFO	2016-11-02 08:32:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:20	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    2s.  Last read position: chr7:82,492,386
INFO	2016-11-02 08:32:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:23	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:    3s.  Last read position: chr7:100,382,464
INFO	2016-11-02 08:32:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:27	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    3s.  Last read position: chr7:114,754,482
INFO	2016-11-02 08:32:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:30	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    3s.  Last read position: chr7:127,053,890
INFO	2016-11-02 08:32:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:33	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    2s.  Last read position: chr7:139,764,756
INFO	2016-11-02 08:32:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:38	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    5s.  Last read position: chr8:12,356,928
INFO	2016-11-02 08:32:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:42	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    3s.  Last read position: chr8:32,810,679
INFO	2016-11-02 08:32:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:45	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    3s.  Last read position: chr8:54,885,723
INFO	2016-11-02 08:32:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:48	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    3s.  Last read position: chr8:72,327,453
INFO	2016-11-02 08:32:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:51	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    3s.  Last read position: chr8:87,247,790
INFO	2016-11-02 08:32:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:32:59	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    8s.  Last read position: chr8:105,254,539
INFO	2016-11-02 08:32:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:03	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:    3s.  Last read position: chr8:117,334,343
INFO	2016-11-02 08:33:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:06	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    2s.  Last read position: chr8:126,053,483
INFO	2016-11-02 08:33:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:09	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:57s.  Time for last 1,000,000:    3s.  Last read position: chr9:21,093,004
INFO	2016-11-02 08:33:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:12	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    3s.  Last read position: chr9:38,532,528
INFO	2016-11-02 08:33:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:17	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    4s.  Last read position: chr9:51,928,100
INFO	2016-11-02 08:33:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:20	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:06:07s.  Time for last 1,000,000:    3s.  Last read position: chr9:63,026,666
INFO	2016-11-02 08:33:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:23	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    3s.  Last read position: chr9:74,896,335
INFO	2016-11-02 08:33:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:26	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:06:14s.  Time for last 1,000,000:    3s.  Last read position: chr9:93,762,330
INFO	2016-11-02 08:33:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:29	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:06:17s.  Time for last 1,000,000:    3s.  Last read position: chr9:107,635,762
INFO	2016-11-02 08:33:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:33	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    3s.  Last read position: chr9:119,891,369
INFO	2016-11-02 08:33:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:36	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:24s.  Time for last 1,000,000:    3s.  Last read position: chr10:13,966,485
INFO	2016-11-02 08:33:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:40	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    3s.  Last read position: chr10:34,189,368
INFO	2016-11-02 08:33:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:43	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:30s.  Time for last 1,000,000:    3s.  Last read position: chr10:52,879,202
INFO	2016-11-02 08:33:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:47	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:34s.  Time for last 1,000,000:    3s.  Last read position: chr10:67,711,921
INFO	2016-11-02 08:33:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:33:59	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:   11s.  Last read position: chr10:80,294,126
INFO	2016-11-02 08:33:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:02	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    3s.  Last read position: chr10:91,615,035
INFO	2016-11-02 08:34:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:05	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    3s.  Last read position: chr10:110,393,041
INFO	2016-11-02 08:34:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:09	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    3s.  Last read position: chr10:125,673,586
INFO	2016-11-02 08:34:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:13	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    3s.  Last read position: chr11:8,684,325
INFO	2016-11-02 08:34:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:16	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:07:04s.  Time for last 1,000,000:    3s.  Last read position: chr11:28,940,988
INFO	2016-11-02 08:34:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:20	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:07:08s.  Time for last 1,000,000:    4s.  Last read position: chr11:46,680,841
INFO	2016-11-02 08:34:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:25	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:07:12s.  Time for last 1,000,000:    4s.  Last read position: chr11:58,884,177
INFO	2016-11-02 08:34:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:29	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    3s.  Last read position: chr11:69,711,184
INFO	2016-11-02 08:34:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:32	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    3s.  Last read position: chr11:78,536,706
INFO	2016-11-02 08:34:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:38	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    6s.  Last read position: chr11:88,556,218
INFO	2016-11-02 08:34:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:42	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    3s.  Last read position: chr11:98,810,136
INFO	2016-11-02 08:34:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:45	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:    3s.  Last read position: chr11:106,968,267
INFO	2016-11-02 08:34:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:49	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:37s.  Time for last 1,000,000:    4s.  Last read position: chr11:117,194,778
INFO	2016-11-02 08:34:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:34:59	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    9s.  Last read position: chr12:8,837,308
INFO	2016-11-02 08:34:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:03	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    4s.  Last read position: chr12:33,543,201
INFO	2016-11-02 08:35:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:06	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:07:54s.  Time for last 1,000,000:    3s.  Last read position: chr12:57,190,251
INFO	2016-11-02 08:35:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:10	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:07:57s.  Time for last 1,000,000:    3s.  Last read position: chr12:77,145,372
INFO	2016-11-02 08:35:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:13	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    3s.  Last read position: chr12:88,797,654
INFO	2016-11-02 08:35:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:17	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    3s.  Last read position: chr12:105,707,808
INFO	2016-11-02 08:35:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:21	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    3s.  Last read position: chr12:119,697,494
INFO	2016-11-02 08:35:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:26	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    4s.  Last read position: chr13:23,684,616
INFO	2016-11-02 08:35:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:29	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:08:16s.  Time for last 1,000,000:    3s.  Last read position: chr13:40,370,233
INFO	2016-11-02 08:35:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:33	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    3s.  Last read position: chr13:52,520,396
INFO	2016-11-02 08:35:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:36	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    3s.  Last read position: chr13:67,522,348
INFO	2016-11-02 08:35:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:40	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    3s.  Last read position: chr13:90,183,702
INFO	2016-11-02 08:35:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:43	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:08:30s.  Time for last 1,000,000:    3s.  Last read position: chr13:104,417,485
INFO	2016-11-02 08:35:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:46	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:08:34s.  Time for last 1,000,000:    3s.  Last read position: chr14:8,318,690
INFO	2016-11-02 08:35:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:49	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    3s.  Last read position: chr14:27,495,164
INFO	2016-11-02 08:35:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:35:56	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    6s.  Last read position: chr14:48,104,078
INFO	2016-11-02 08:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:00	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    3s.  Last read position: chr14:62,683,653
INFO	2016-11-02 08:36:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:03	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    3s.  Last read position: chr14:75,797,295
INFO	2016-11-02 08:36:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:06	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    3s.  Last read position: chr14:101,360,545
INFO	2016-11-02 08:36:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:09	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    3s.  Last read position: chr14:122,194,794
INFO	2016-11-02 08:36:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:14	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    4s.  Last read position: chr15:27,506,180
INFO	2016-11-02 08:36:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:17	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:09:05s.  Time for last 1,000,000:    3s.  Last read position: chr15:51,874,704
INFO	2016-11-02 08:36:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:21	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:    3s.  Last read position: chr15:69,616,178
INFO	2016-11-02 08:36:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:24	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:09:11s.  Time for last 1,000,000:    3s.  Last read position: chr15:80,256,152
INFO	2016-11-02 08:36:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:28	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:09:15s.  Time for last 1,000,000:    3s.  Last read position: chr15:91,014,362
INFO	2016-11-02 08:36:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:31	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:09:19s.  Time for last 1,000,000:    3s.  Last read position: chr15:102,052,497
INFO	2016-11-02 08:36:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:34	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    3s.  Last read position: chr16:14,453,422
INFO	2016-11-02 08:36:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:38	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    3s.  Last read position: chr16:29,798,501
INFO	2016-11-02 08:36:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:41	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    2s.  Last read position: chr16:43,290,058
INFO	2016-11-02 08:36:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:44	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    3s.  Last read position: chr16:63,593,214
INFO	2016-11-02 08:36:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:52	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:09:40s.  Time for last 1,000,000:    8s.  Last read position: chr16:90,493,764
INFO	2016-11-02 08:36:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:55	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    3s.  Last read position: chr17:6,885,732
INFO	2016-11-02 08:36:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:36:58	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    3s.  Last read position: chr17:25,419,409
INFO	2016-11-02 08:36:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:01	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:09:49s.  Time for last 1,000,000:    3s.  Last read position: chr17:32,965,541
INFO	2016-11-02 08:37:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:06	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:    4s.  Last read position: chr17:43,543,093
INFO	2016-11-02 08:37:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:09	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:09:56s.  Time for last 1,000,000:    3s.  Last read position: chr17:56,317,877
INFO	2016-11-02 08:37:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:12	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:09:59s.  Time for last 1,000,000:    2s.  Last read position: chr17:73,494,591
INFO	2016-11-02 08:37:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:15	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:10:02s.  Time for last 1,000,000:    3s.  Last read position: chr17:87,372,037
INFO	2016-11-02 08:37:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:18	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    3s.  Last read position: chr18:16,906,850
INFO	2016-11-02 08:37:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:21	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:10:08s.  Time for last 1,000,000:    3s.  Last read position: chr18:36,563,212
INFO	2016-11-02 08:37:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:24	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:    3s.  Last read position: chr18:56,415,421
INFO	2016-11-02 08:37:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:27	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    2s.  Last read position: chr18:69,988,519
INFO	2016-11-02 08:37:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:30	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    3s.  Last read position: chr18:84,974,279
INFO	2016-11-02 08:37:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:33	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:10:20s.  Time for last 1,000,000:    2s.  Last read position: chr19:10,893,673
INFO	2016-11-02 08:37:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:40	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:10:27s.  Time for last 1,000,000:    6s.  Last read position: chr19:29,363,978
INFO	2016-11-02 08:37:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:43	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    2s.  Last read position: chr19:43,614,446
INFO	2016-11-02 08:37:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:46	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:    3s.  Last read position: chr19:56,333,258
INFO	2016-11-02 08:37:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:50	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:10:37s.  Time for last 1,000,000:    3s.  Last read position: chrX:42,029,887
INFO	2016-11-02 08:37:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:52	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    2s.  Last read position: chrX:98,776,856
INFO	2016-11-02 08:37:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:56	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:10:43s.  Time for last 1,000,000:    3s.  Last read position: chrX:151,919,351
INFO	2016-11-02 08:37:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-02 08:37:58	MarkDuplicates	Read 152723480 records. 0 pairs never matched.
INFO	2016-11-02 08:37:59	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2468172728; totalMemory: 2554855424; maxMemory: 3817865216
INFO	2016-11-02 08:37:59	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-02 08:37:59	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-02 08:37:59	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-02 08:38:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-02 08:38:59	MarkDuplicates	After generateDuplicateIndexes freeMemory: 3559291840; totalMemory: 3587178496; maxMemory: 3817865216
INFO	2016-11-02 08:38:59	MarkDuplicates	Marking 143277910 records as duplicates.
INFO	2016-11-02 08:38:59	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-11-02 08:40:48	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:49s.  Time for last 10,000,000:  109s.  Last read position: chr1:182,254,747
INFO	2016-11-02 08:42:37	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:38s.  Time for last 10,000,000:  109s.  Last read position: chr2:137,330,271
INFO	2016-11-02 08:44:35	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:35s.  Time for last 10,000,000:  117s.  Last read position: chr3:127,621,534
INFO	2016-11-02 08:46:22	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:07:22s.  Time for last 10,000,000:  107s.  Last read position: chr4:140,257,389
INFO	2016-11-02 08:48:08	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:09:08s.  Time for last 10,000,000:  105s.  Last read position: chr5:140,701,524
INFO	2016-11-02 08:49:55	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:55s.  Time for last 10,000,000:  106s.  Last read position: chr7:16,358,951
INFO	2016-11-02 08:51:43	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:12:43s.  Time for last 10,000,000:  108s.  Last read position: chr8:32,810,679
INFO	2016-11-02 08:53:43	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:14:43s.  Time for last 10,000,000:  120s.  Last read position: chr9:63,026,666
INFO	2016-11-02 08:55:49	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:16:49s.  Time for last 10,000,000:  125s.  Last read position: chr10:91,615,035
INFO	2016-11-02 08:57:50	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:18:50s.  Time for last 10,000,000:  121s.  Last read position: chr11:98,810,136
INFO	2016-11-02 08:59:37	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:20:37s.  Time for last 10,000,000:  106s.  Last read position: chr13:23,684,616
INFO	2016-11-02 09:01:23	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:22:23s.  Time for last 10,000,000:  105s.  Last read position: chr14:75,797,295
INFO	2016-11-02 09:03:12	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:24:12s.  Time for last 10,000,000:  109s.  Last read position: chr16:29,798,501
INFO	2016-11-02 09:05:10	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:26:10s.  Time for last 10,000,000:  118s.  Last read position: chr17:87,372,037
INFO	2016-11-02 09:07:19	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:28:19s.  Time for last 10,000,000:  128s.  Last read position: chrX:42,029,887
Could not delete file /tmp/imk1/sortingcollection.7544014339463482276.tmp
Could not delete file /tmp/imk1/sortingcollection.4496677946893998476.tmp
INFO	2016-11-02 09:07:51	MarkDuplicates	Before output close freeMemory: 3682476456; totalMemory: 3713007616; maxMemory: 3817865216
INFO	2016-11-02 09:07:51	MarkDuplicates	After output close freeMemory: 3682475640; totalMemory: 3713007616; maxMemory: 3817865216
[Wed Nov 02 09:07:51 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 40.66 minutes.
Runtime.totalMemory()=3713007616

 

 
# 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/SRR836483/out/align/rep1/SRR836483.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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/SRR836483/out/qc/rep1/SRR836483.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--------------------
47350 (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/SRR836483/out/align/rep1/SRR836483.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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--------------------
48067 (process ID) old priority 0, new priority 10

Waiting for 32 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/SRR836483/out/align/rep1/SRR836483.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.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--------------------
48175 (process ID) old priority 0, new priority 10
Waiting for 45 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/SRR836483/out/align/rep1/SRR836483.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/SRR836483/out/align/rep1/SRR836483.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/rep1/SRR836483.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr2/SRR836483.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/align/pseudo_reps/rep1/pr1/SRR836483.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--------------------
48174 (process ID) old priority 0, new priority 10
Waiting for 41 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/SRR836483/out/align/rep1/SRR836483.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/out/qc/rep1/SRR836483.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
 

     
--------------------Post mortem info--------------------
==============================================================
job_number:                 3337
exec_file:                  job_scripts/3337
submission_time:            Wed Nov  2 09:28:57 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/SRR836483
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836483/chipseq.bds.20161101_222025_262_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/SRR836483/chipseq.bds.20161101_222025_262_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=36589.SRR836483.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/SRR836483,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 51178 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
parallel environment:  shm range: 4
usage    1:                 cpu=00:00:00, mem=0.01401 GBs, io=0.00545, vmem=159.535M, maxvmem=159.535M
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