spp rep1

 chipseq.bds.20160928_164801_472/task.callpeak_spp.spp_rep1.line_54.id_25
 

 chipseq.bds.20160928_164801_472_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20160928_164801_472_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20160928_164801_472_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
chipseq.bds.20160928_164801_472_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
chipseq.bds.20160928_164801_472_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
chipseq.bds.20160928_164801_472_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
 

 chipseq.bds.20160928_164801_472_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20160928_164801_472_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20160928_164801_472_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF7_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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--------------------
11882 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[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... 74.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.00 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.78 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... 94.49 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.14 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.15 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.17 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.11 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.25 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.81 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.86 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... 83.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.79 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... 75.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.52 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.68 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.90 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.36 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... 56.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.99 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... 78.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.74 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... 87.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.23 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.28 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.69 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... 83.54 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... 96.70 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.48 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.34 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.33 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.42 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... 91.51 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... 114.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.56 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.34 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... 86.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.04 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... 88.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.45 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... 84.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.17 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.02 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... 84.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.04 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... 98.06 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... 94.62 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.84 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... 88.72 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.51 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.49 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.17 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... 103.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.80 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... 101.04 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.09 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... 87.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.16 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... 103.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.15 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.15 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.63 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.09 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.55 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... 87.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.34 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.76 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... 85.97 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.22 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.81 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.48 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.94 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... 95.04 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.44 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.24 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.48 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.54 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... 89.47 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.06 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... 82.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.07 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.60 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.18 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.27 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.36 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.40 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... 84.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.49 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... 90.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.29 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... 85.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.84 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... 91.04 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.47 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... 75.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.53 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.57 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... 71.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.66 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... 78.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.45 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... 76.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.84 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.62 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... 85.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.75 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... 78.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.95 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... 85.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.47 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.38 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.13 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... 83.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.77 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.84 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... 82.58 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... 75.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.99 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... 86.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.55 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... 83.95 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... 91.53 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... 85.14 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... 81.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.33 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... 80.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.88 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... 96.39 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... 94.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.75 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... 86.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.27 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.83 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.52 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.60 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... 90.62 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.28 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.14 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... 75.39 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... 94.99 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.11 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.68 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.57 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.30 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.37 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... 82.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.06 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... 76.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.49 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... 78.49 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... 80.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.77 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... 80.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.59 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.34 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.65 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... 81.72 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... 79.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.84 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... 83.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.08 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.76 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.31 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.71 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.41 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.64 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.35 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.54 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... 81.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.97 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... 90.18 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... 82.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.63 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... 76.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.76 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... 86.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.33 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.54 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... 134.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.28 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.57 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.30 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... 97.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.46 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.80 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... 68.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.12 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.85 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... 61.26 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... 62.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.88 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... 55.74 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... 62.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.1% 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] 106168320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.55 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... 72.67 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.83 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... 59.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.0% 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] 108265472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.77 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... 62.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.68 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.04 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 77.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.60 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... 63.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.08 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... 65.85 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... 78.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.29 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.73 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... 60.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.02 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... 66.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.79 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... 60.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.77 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... 60.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.51 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... 61.66 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... 63.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.65 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... 72.29 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... 69.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.61 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... 64.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.32 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... 56.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.01 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... 85.70 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... 73.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.75 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... 57.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.58 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.04 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... 67.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.66 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.43 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.76 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... 63.50 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... 67.12 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... 66.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.03 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... 62.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.71 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... 67.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.2% 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] 142868480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.35 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... 60.36 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... 71.88 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.0% 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] 147587072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.84 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... 58.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.45 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... 62.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.98 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... 67.37 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... 61.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.78 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... 81.95 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.79 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.92 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... 77.70 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... 65.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.01 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.47 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... 53.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.12 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... 49.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.68 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.80 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... 56.42 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... 66.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.65 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... 68.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.30 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... 73.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.84 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... 204.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.16 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.24 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.03 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.31 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.87 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... 146.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.58 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.29 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... 143.62 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... 130.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.15 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.91 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.40 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.06 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... 58.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.09 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... 59.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.86 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... 69.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.78 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... 67.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.77 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.81 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... 67.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.90 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.27 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.95 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.73 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... 66.16 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... 72.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.52 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.10 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... 62.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.35 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... 60.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.58 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.14 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.61 sec
[bwa_aln_core] write to the disk... 0.10 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.75 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 0.1% 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] 185335808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 190316544 sequences have been processed.
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[bwa_aln_core] calculate SA coordinate... 55.93 sec
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[bwa_aln_core] 212860928 sequences have been processed.
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[bwa_aln_core] 216006656 sequences have been processed.
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[bwa_aln_core] 216530944 sequences have been processed.
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[bwa_aln_core] 216793088 sequences have been processed.
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[bwa_aln_core] 217317376 sequences have been processed.
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[bwa_aln_core] 217841664 sequences have been processed.
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[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.71 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.4% 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] 240386048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.01 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.09 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 247726080 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] 247988224 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.17 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 97.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 249298944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 249823232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 250347520 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.29 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 250609664 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 250871808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 251133952 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 251396096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 251658240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 251920384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.47 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 252182528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.97 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 252444672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 252642739 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/ZF7_allReps.fastq.gz
[main] Real time: 23231.688 sec; CPU: 75330.227 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/mousePrimaryBCellInput.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.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--------------------
2838 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.01 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.19 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.21 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.23 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.21 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.28 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.28 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.35 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.23 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.23 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.16 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.25 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.15 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.04 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.77 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.24 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.07 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.17 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.15 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.19 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.06 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.03 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.14 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.99 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.12 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.29 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.34 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.32 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.30 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.46 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.44 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.53 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.17 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.46 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.44 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.24 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.43 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.82 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.98 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.08 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.81 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.46 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.45 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.23 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 22.58 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.55 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.19 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.89 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.69 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 19.00 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.93 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 5.35 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 23141323 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/mousePrimaryBCellInput.fastq.gz
[main] Real time: 1829.632 sec; CPU: 1829.504 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
31737 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.48 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.71 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.92 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.70 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.42 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.38 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.52 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.61 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.98 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.80 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.66 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.30 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.63 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.42 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.26 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.55 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.51 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.64 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.57 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.01 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.53 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.13 sec
[bwa_aln_core] 23141323 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 552.632 sec; CPU: 464.508 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.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/ZF7/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.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--------------------
3934 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ctl1/mousePrimaryBCellInput.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
10419 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Sep 28 17:39:42 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ctl1/mousePrimaryBCellInput.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 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 Sep 28 17:39:42 PDT 2016] Executing as imk1@surya on Linux 4.2.0-27-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-28 17:39:43	MarkDuplicates	Start of doWork freeMemory: 255390112; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 17:39:43	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 17:39:43	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 17:39:53	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    9s.  Last read position: chr1:174,151,470
INFO	2016-09-28 17:39:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:00	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    6s.  Last read position: chr2:135,780,411
INFO	2016-09-28 17:40:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:06	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    5s.  Last read position: chr3:122,530,375
INFO	2016-09-28 17:40:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:13	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    7s.  Last read position: chr4:135,044,888
INFO	2016-09-28 17:40:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:17	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr5:135,067,778
INFO	2016-09-28 17:40:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:21	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    4s.  Last read position: chr6:144,681,933
INFO	2016-09-28 17:40:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:26	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    4s.  Last read position: chr8:12,749,386
INFO	2016-09-28 17:40:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:28	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    2s.  Last read position: chr9:42,425,131
INFO	2016-09-28 17:40:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:30	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    2s.  Last read position: chr10:69,658,983
INFO	2016-09-28 17:40:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:36	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    5s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:40:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:38	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    2s.  Last read position: chr13:6,026,344
INFO	2016-09-28 17:40:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:41	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr14:54,434,282
INFO	2016-09-28 17:40:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:43	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    2s.  Last read position: chr15:98,839,731
INFO	2016-09-28 17:40:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:48	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    4s.  Last read position: chr17:62,456,013
INFO	2016-09-28 17:40:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:50	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,585,732
INFO	2016-09-28 17:40:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:40:58	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 17:40:58	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2469682384; totalMemory: 2556100608; maxMemory: 3817799680
INFO	2016-09-28 17:40:58	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 17:40:58	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 17:40:58	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 17:41:01	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 17:41:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1838489000; totalMemory: 2814509056; maxMemory: 3817799680
INFO	2016-09-28 17:41:02	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 17:41:02	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 17:42:26	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:24s.  Time for last 10,000,000:   84s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:43:11	MarkDuplicates	Before output close freeMemory: 2868564704; totalMemory: 2896429056; maxMemory: 3817799680
INFO	2016-09-28 17:43:11	MarkDuplicates	After output close freeMemory: 2896744344; totalMemory: 2924609536; maxMemory: 3817799680
[Wed Sep 28 17:43:11 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.48 minutes.
Runtime.totalMemory()=2924609536

 

 
# 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.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/ZF7/out/qc/ctl1/mousePrimaryBCellInput.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--------------------
10888 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.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--------------------
11564 (process ID) old priority 0, new priority 10

Waiting for 23 seconds.

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF7_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.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--------------------
36359 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.34 sec
[bwa_aln_core] refine gapped alignments... 8.77 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.82 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.36 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.94 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.91 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.54 sec
[bwa_aln_core] refine gapped alignments... 5.67 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.85 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.01 sec
[bwa_aln_core] refine gapped alignments... 7.20 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.12 sec
[bwa_aln_core] refine gapped alignments... 7.99 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.39 sec
[bwa_aln_core] refine gapped alignments... 7.15 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.72 sec
[bwa_aln_core] refine gapped alignments... 6.14 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.12 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.46 sec
[bwa_aln_core] refine gapped alignments... 6.20 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.60 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.84 sec
[bwa_aln_core] refine gapped alignments... 6.17 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.48 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.16 sec
[bwa_aln_core] refine gapped alignments... 6.45 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.37 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.02 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.41 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.85 sec
[bwa_aln_core] refine gapped alignments... 4.23 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.32 sec
[bwa_aln_core] refine gapped alignments... 8.16 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.97 sec
[bwa_aln_core] refine gapped alignments... 8.47 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.69 sec
[bwa_aln_core] refine gapped alignments... 4.81 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.07 sec
[bwa_aln_core] refine gapped alignments... 4.46 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.51 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.81 sec
[bwa_aln_core] refine gapped alignments... 8.60 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.18 sec
[bwa_aln_core] refine gapped alignments... 7.54 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.62 sec
[bwa_aln_core] refine gapped alignments... 3.86 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.90 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.94 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.03 sec
[bwa_aln_core] refine gapped alignments... 2.19 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.62 sec
[bwa_aln_core] refine gapped alignments... 6.20 sec
[bwa_aln_core] print alignments... 1.21 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.94 sec
[bwa_aln_core] refine gapped alignments... 6.86 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.51 sec
[bwa_aln_core] refine gapped alignments... 6.18 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.92 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.58 sec
[bwa_aln_core] refine gapped alignments... 7.22 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.83 sec
[bwa_aln_core] refine gapped alignments... 5.90 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.09 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.60 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.65 sec
[bwa_aln_core] refine gapped alignments... 6.29 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.56 sec
[bwa_aln_core] refine gapped alignments... 8.25 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.69 sec
[bwa_aln_core] refine gapped alignments... 8.89 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.95 sec
[bwa_aln_core] refine gapped alignments... 7.13 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.69 sec
[bwa_aln_core] refine gapped alignments... 8.33 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.87 sec
[bwa_aln_core] refine gapped alignments... 6.16 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.63 sec
[bwa_aln_core] refine gapped alignments... 6.17 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.24 sec
[bwa_aln_core] refine gapped alignments... 7.69 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.13 sec
[bwa_aln_core] refine gapped alignments... 6.10 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.29 sec
[bwa_aln_core] refine gapped alignments... 7.72 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.00 sec
[bwa_aln_core] refine gapped alignments... 6.20 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... 37.96 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.16 sec
[bwa_aln_core] refine gapped alignments... 6.62 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.04 sec
[bwa_aln_core] refine gapped alignments... 6.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.54 sec
[bwa_aln_core] refine gapped alignments... 6.18 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.26 sec
[bwa_aln_core] refine gapped alignments... 6.10 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.70 sec
[bwa_aln_core] refine gapped alignments... 5.91 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.63 sec
[bwa_aln_core] refine gapped alignments... 6.02 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.18 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.22 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.03 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.79 sec
[bwa_aln_core] refine gapped alignments... 6.29 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.46 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.53 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.32 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.65 sec
[bwa_aln_core] refine gapped alignments... 5.61 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.73 sec
[bwa_aln_core] refine gapped alignments... 5.83 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.30 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.32 sec
[bwa_aln_core] refine gapped alignments... 6.00 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.04 sec
[bwa_aln_core] refine gapped alignments... 5.98 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.86 sec
[bwa_aln_core] refine gapped alignments... 6.10 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.49 sec
[bwa_aln_core] refine gapped alignments... 6.14 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.09 sec
[bwa_aln_core] refine gapped alignments... 6.31 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.13 sec
[bwa_aln_core] refine gapped alignments... 6.21 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.08 sec
[bwa_aln_core] refine gapped alignments... 6.04 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.53 sec
[bwa_aln_core] refine gapped alignments... 6.31 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.42 sec
[bwa_aln_core] refine gapped alignments... 6.10 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.22 sec
[bwa_aln_core] refine gapped alignments... 6.20 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 5.98 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.62 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.79 sec
[bwa_aln_core] refine gapped alignments... 6.19 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.04 sec
[bwa_aln_core] refine gapped alignments... 6.42 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... 37.73 sec
[bwa_aln_core] refine gapped alignments... 5.87 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.63 sec
[bwa_aln_core] refine gapped alignments... 5.91 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.22 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.30 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.56 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.98 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.73 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.57 sec
[bwa_aln_core] refine gapped alignments... 6.31 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.58 sec
[bwa_aln_core] refine gapped alignments... 6.16 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.85 sec
[bwa_aln_core] refine gapped alignments... 6.12 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.95 sec
[bwa_aln_core] refine gapped alignments... 6.15 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.48 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.91 sec
[bwa_aln_core] refine gapped alignments... 6.26 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.34 sec
[bwa_aln_core] refine gapped alignments... 5.92 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.11 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.15 sec
[bwa_aln_core] refine gapped alignments... 5.86 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.88 sec
[bwa_aln_core] refine gapped alignments... 6.21 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.38 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.36 sec
[bwa_aln_core] refine gapped alignments... 6.18 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... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.34 sec
[bwa_aln_core] refine gapped alignments... 6.31 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.50 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.62 sec
[bwa_aln_core] refine gapped alignments... 6.19 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.52 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.43 sec
[bwa_aln_core] refine gapped alignments... 6.26 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.41 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.35 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.94 sec
[bwa_aln_core] refine gapped alignments... 6.13 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.39 sec
[bwa_aln_core] refine gapped alignments... 6.26 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.57 sec
[bwa_aln_core] refine gapped alignments... 6.15 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.71 sec
[bwa_aln_core] refine gapped alignments... 6.27 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.87 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.65 sec
[bwa_aln_core] refine gapped alignments... 6.31 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.61 sec
[bwa_aln_core] refine gapped alignments... 9.09 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.86 sec
[bwa_aln_core] refine gapped alignments... 6.26 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.05 sec
[bwa_aln_core] refine gapped alignments... 6.27 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.48 sec
[bwa_aln_core] refine gapped alignments... 6.23 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.13 sec
[bwa_aln_core] refine gapped alignments... 6.34 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.21 sec
[bwa_aln_core] refine gapped alignments... 7.64 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.62 sec
[bwa_aln_core] refine gapped alignments... 7.14 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.10 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.09 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.92 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.50 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.58 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.56 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... 5.71 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.50 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.04 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.60 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.70 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.83 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.75 sec
[bwa_aln_core] refine gapped alignments... 4.84 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.20 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.00 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.91 sec
[bwa_aln_core] refine gapped alignments... 4.11 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.44 sec
[bwa_aln_core] refine gapped alignments... 3.58 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.41 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.07 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.14 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.57 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.02 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.34 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.81 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.51 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.75 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.28 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.01 sec
[bwa_aln_core] refine gapped alignments... 1.75 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 6.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.94 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.38 sec
[bwa_aln_core] refine gapped alignments... 6.73 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.35 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.36 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.95 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.97 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.62 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 43778048 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... 0.57 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.76 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.59 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.89 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.83 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.42 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.37 sec
[bwa_aln_core] refine gapped alignments... 1.76 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.04 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.13 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.17 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.15 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.82 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.84 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.15 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.19 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.69 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.74 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.21 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.30 sec
[bwa_aln_core] refine gapped alignments... 6.05 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.62 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.63 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 49807360 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... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.04 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.17 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.08 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.92 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.89 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.06 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.50 sec
[bwa_aln_core] refine gapped alignments... 3.28 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.82 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.13 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.54 sec
[bwa_aln_core] refine gapped alignments... 1.28 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.20 sec
[bwa_aln_core] refine gapped alignments... 3.30 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.30 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 1.64 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 6.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 5.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.74 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 4.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.58 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.61 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.10 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.73 sec
[bwa_aln_core] refine gapped alignments... 2.18 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.47 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.73 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.45 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.15 sec
[bwa_aln_core] refine gapped alignments... 4.69 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 57409536 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... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.98 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.31 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.20 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.87 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.27 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.16 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.15 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.34 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.27 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.12 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.92 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.55 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... 11.65 sec
[bwa_aln_core] refine gapped alignments... 5.53 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... 10.90 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.52 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.64 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.57 sec
[bwa_aln_core] refine gapped alignments... 2.78 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.36 sec
[bwa_aln_core] refine gapped alignments... 6.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.50 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.91 sec
[bwa_aln_core] refine gapped alignments... 6.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.09 sec
[bwa_aln_core] refine gapped alignments... 5.79 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.77 sec
[bwa_aln_core] refine gapped alignments... 5.88 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.51 sec
[bwa_aln_core] refine gapped alignments... 4.89 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.73 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.47 sec
[bwa_aln_core] refine gapped alignments... 4.83 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.10 sec
[bwa_aln_core] refine gapped alignments... 5.85 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 3.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.18 sec
[bwa_aln_core] refine gapped alignments... 4.98 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 3.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.19 sec
[bwa_aln_core] refine gapped alignments... 6.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.52 sec
[bwa_aln_core] refine gapped alignments... 6.19 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.25 sec
[bwa_aln_core] refine gapped alignments... 5.30 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 3.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.06 sec
[bwa_aln_core] refine gapped alignments... 6.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.14 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.58 sec
[bwa_aln_core] refine gapped alignments... 3.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.93 sec
[bwa_aln_core] refine gapped alignments... 5.60 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.28 sec
[bwa_aln_core] refine gapped alignments... 5.04 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.70 sec
[bwa_aln_core] refine gapped alignments... 4.99 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.52 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.32 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.28 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.33 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.68 sec
[bwa_aln_core] refine gapped alignments... 5.77 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.49 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.01 sec
[bwa_aln_core] refine gapped alignments... 4.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.91 sec
[bwa_aln_core] refine gapped alignments... 6.20 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.98 sec
[bwa_aln_core] refine gapped alignments... 6.03 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.05 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.88 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.46 sec
[bwa_aln_core] refine gapped alignments... 6.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.88 sec
[bwa_aln_core] refine gapped alignments... 5.34 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.24 sec
[bwa_aln_core] refine gapped alignments... 4.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.79 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.30 sec
[bwa_aln_core] refine gapped alignments... 6.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.09 sec
[bwa_aln_core] refine gapped alignments... 6.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.18 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 9.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.97 sec
[bwa_aln_core] refine gapped alignments... 6.44 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... 38.66 sec
[bwa_aln_core] refine gapped alignments... 6.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.16 sec
[bwa_aln_core] refine gapped alignments... 6.06 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.34 sec
[bwa_aln_core] refine gapped alignments... 6.21 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.64 sec
[bwa_aln_core] refine gapped alignments... 5.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.95 sec
[bwa_aln_core] refine gapped alignments... 4.32 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... 39.16 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.92 sec
[bwa_aln_core] refine gapped alignments... 6.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.34 sec
[bwa_aln_core] refine gapped alignments... 4.98 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.25 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.38 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.91 sec
[bwa_aln_core] refine gapped alignments... 5.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.85 sec
[bwa_aln_core] refine gapped alignments... 5.36 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... 37.23 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.78 sec
[bwa_aln_core] refine gapped alignments... 6.60 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.05 sec
[bwa_aln_core] refine gapped alignments... 3.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.90 sec
[bwa_aln_core] refine gapped alignments... 4.83 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.45 sec
[bwa_aln_core] refine gapped alignments... 6.35 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.76 sec
[bwa_aln_core] refine gapped alignments... 4.94 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.63 sec
[bwa_aln_core] refine gapped alignments... 6.06 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.71 sec
[bwa_aln_core] refine gapped alignments... 6.26 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.02 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.29 sec
[bwa_aln_core] refine gapped alignments... 6.58 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.61 sec
[bwa_aln_core] refine gapped alignments... 4.22 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.65 sec
[bwa_aln_core] refine gapped alignments... 6.40 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.30 sec
[bwa_aln_core] refine gapped alignments... 6.21 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.60 sec
[bwa_aln_core] refine gapped alignments... 6.27 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.64 sec
[bwa_aln_core] refine gapped alignments... 6.23 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.05 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.40 sec
[bwa_aln_core] refine gapped alignments... 4.83 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.47 sec
[bwa_aln_core] refine gapped alignments... 4.36 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.32 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.80 sec
[bwa_aln_core] refine gapped alignments... 4.44 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.85 sec
[bwa_aln_core] refine gapped alignments... 4.13 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.15 sec
[bwa_aln_core] refine gapped alignments... 5.80 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.67 sec
[bwa_aln_core] refine gapped alignments... 5.68 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.99 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.96 sec
[bwa_aln_core] refine gapped alignments... 5.36 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.78 sec
[bwa_aln_core] refine gapped alignments... 6.14 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.91 sec
[bwa_aln_core] refine gapped alignments... 5.97 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.14 sec
[bwa_aln_core] refine gapped alignments... 5.31 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.76 sec
[bwa_aln_core] refine gapped alignments... 4.61 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.96 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.69 sec
[bwa_aln_core] refine gapped alignments... 3.56 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.99 sec
[bwa_aln_core] refine gapped alignments... 3.41 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.24 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.21 sec
[bwa_aln_core] refine gapped alignments... 3.36 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.43 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.94 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.34 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.39 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.12 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.87 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.91 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.06 sec
[bwa_aln_core] refine gapped alignments... 3.25 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.14 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.74 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.00 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.01 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.17 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.71 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.31 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.59 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.97 sec
[bwa_aln_core] refine gapped alignments... 4.12 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.91 sec
[bwa_aln_core] refine gapped alignments... 2.82 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.86 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.88 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.16 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.52 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... 13.47 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.45 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.31 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.79 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.38 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.13 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.76 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.70 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.19 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.69 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.33 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.21 sec
[bwa_aln_core] refine gapped alignments... 3.31 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.98 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.25 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.26 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.38 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.53 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.70 sec
[bwa_aln_core] refine gapped alignments... 0.51 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... 27.73 sec
[bwa_aln_core] refine gapped alignments... 1.20 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.39 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.54 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.76 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.72 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.44 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.35 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.47 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.12 sec
[bwa_aln_core] refine gapped alignments... 2.81 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.58 sec
[bwa_aln_core] refine gapped alignments... 3.81 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.20 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.35 sec
[bwa_aln_core] refine gapped alignments... 3.87 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.05 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.75 sec
[bwa_aln_core] refine gapped alignments... 1.71 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.24 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.82 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 9.84 sec
[bwa_aln_core] refine gapped alignments... 1.09 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.78 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.71 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.36 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.28 sec
[bwa_aln_core] refine gapped alignments... 3.80 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.07 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.71 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.94 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.71 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.58 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.61 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.97 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.41 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.06 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.45 sec
[bwa_aln_core] refine gapped alignments... 4.78 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.52 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.51 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.06 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.01 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.91 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.26 sec
[bwa_aln_core] refine gapped alignments... 0.90 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.56 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.24 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.06 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.15 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.78 sec
[bwa_aln_core] refine gapped alignments... 6.06 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.05 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 7.99 sec
[bwa_aln_core] refine gapped alignments... 2.35 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.10 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.62 sec
[bwa_aln_core] refine gapped alignments... 3.19 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.83 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.92 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.68 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.15 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.0% 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... 0.53 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.40 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.68 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.39 sec
[bwa_aln_core] refine gapped alignments... 3.93 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 6.32 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.59 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.31 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.49 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 2.75 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.85 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.12 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.30 sec
[bwa_aln_core] refine gapped alignments... 0.51 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... 26.75 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.55 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.57 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 121634816 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... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.41 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.12 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 122421248 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... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.01 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 23.54 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.91 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.03 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.03 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.17 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.32 sec
[bwa_aln_core] refine gapped alignments... 1.01 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... 31.42 sec
[bwa_aln_core] refine gapped alignments... 0.52 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... 28.14 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.56 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.04 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.70 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.78 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.95 sec
[bwa_aln_core] refine gapped alignments... 5.65 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.37 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.13 sec
[bwa_aln_core] refine gapped alignments... 5.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.93 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.09 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.20 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 20.03 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.68 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.08 sec
[bwa_aln_core] refine gapped alignments... 6.06 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.73 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.58 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.54 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.29 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.65 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.35 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.68 sec
[bwa_aln_core] refine gapped alignments... 4.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.68 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.49 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.20 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.83 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 133955584 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... 0.62 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.16 sec
[bwa_aln_core] refine gapped alignments... 5.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.16 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 13.97 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 3.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.13 sec
[bwa_aln_core] refine gapped alignments... 1.17 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.54 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.17 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 2.06 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.71 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.96 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.31 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.21 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.06 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.61 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.70 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.28 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.14 sec
[bwa_aln_core] refine gapped alignments... 3.25 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 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... 19.28 sec
[bwa_aln_core] refine gapped alignments... 2.92 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.53 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.81 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.93 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.32 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.28 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.56 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.62 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.59 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.85 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.93 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.68 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.33 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.23 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.29 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.68 sec
[bwa_aln_core] refine gapped alignments... 3.73 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 3.59 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.04 sec
[bwa_aln_core] refine gapped alignments... 3.25 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.05 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.06 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.43 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.09 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.46 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.80 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.04 sec
[bwa_aln_core] refine gapped alignments... 3.00 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.52 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.18 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.27 sec
[bwa_aln_core] refine gapped alignments... 2.76 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... 8.42 sec
[bwa_aln_core] refine gapped alignments... 2.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.40 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.12 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 20.43 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.67 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.50 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.04 sec
[bwa_aln_core] refine gapped alignments... 0.52 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... 26.67 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.53 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.40 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.23 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.70 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.56 sec
[bwa_aln_core] refine gapped alignments... 3.87 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.50 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.62 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.80 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 0.52 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... 5.51 sec
[bwa_aln_core] refine gapped alignments... 0.66 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... 27.42 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.06 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.12 sec
[bwa_aln_core] refine gapped alignments... 0.85 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 3.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.81 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.65 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.11 sec
[bwa_aln_core] refine gapped alignments... 0.70 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 3.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.51 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... 9.08 sec
[bwa_aln_core] refine gapped alignments... 0.49 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... 11.01 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.91 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.16 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.10 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.95 sec
[bwa_aln_core] refine gapped alignments... 0.49 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... 15.58 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.06 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.83 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.65 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.62 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.91 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 162004992 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... 0.57 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 1.50 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.50 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.39 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.24 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.94 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.76 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.28 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.28 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.68 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.36 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 165675008 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... 0.49 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... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.49 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... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.69 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.49 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.04 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.48 sec
[bwa_aln_core] refine gapped alignments... 4.53 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.11 sec
[bwa_aln_core] refine gapped alignments... 0.63 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.18 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.82 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.43 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.06 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.96 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 171966464 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... 0.51 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.97 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.56 sec
[bwa_aln_core] refine gapped alignments... 0.50 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... 8.01 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.62 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.57 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.63 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.29 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.53 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.95 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.84 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.48 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.78 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.17 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.88 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.66 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.99 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.19 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.22 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.68 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.10 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.70 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.39 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.20 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.51 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.41 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.88 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.33 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.70 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.33 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.30 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.37 sec
[bwa_aln_core] refine gapped alignments... 2.80 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.49 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.36 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.92 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.34 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.33 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.54 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.30 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.76 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.23 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 196083712 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.41 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.49 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.78 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.90 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.06 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.92 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.15 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.23 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.62 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
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[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.77 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.37 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.45 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
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[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.32 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.94 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.08 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.62 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.48 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.64 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.91 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.74 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.45 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.45 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.42 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.39 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.33 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.90 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.12 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.49 sec
[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
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[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
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[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.96 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 216793088 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.78 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.89 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
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[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.08 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.99 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.06 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
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[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.59 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.97 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.97 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.95 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.02 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.16 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.09 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.24 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.48 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.49 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.71 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.25 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.61 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.05 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.29 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.20 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.20 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.72 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.53 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.31 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.20 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.76 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.08 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.86 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.28 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.39 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.40 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.40 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.35 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.32 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.25 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.23 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 237764608 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.16 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.47 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 238288896 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... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.89 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.90 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.01 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.11 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.18 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.94 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.93 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.98 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.67 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.12 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.65 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.13 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.78 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.97 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.97 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 246153216 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... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.86 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.17 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 247726080 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.03 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 247988224 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.12 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.10 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.05 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.02 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 249298944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.53 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 249823232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.83 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 250347520 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 250609664 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... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 250871808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 251133952 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 251396096 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.91 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 251658240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 251920384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 252182528 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 252444672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.23 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.24 sec
[bwa_aln_core] 252642739 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/ZF7/out/align/rep1/ZF7_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF7_allReps.fastq.gz
[main] Real time: 19683.057 sec; CPU: 19128.456 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 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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/ZF7/out/align/rep1/ZF7_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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--------------------
18140 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.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--------------------
6253 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Sep 29 05:30:07 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 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
[Thu Sep 29 05:30:07 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-29 05:30:08	MarkDuplicates	Start of doWork freeMemory: 255390328; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-29 05:30:08	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-29 05:30:08	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-29 05:30:11	AbstractDuplicateFindingAlgorithm	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	2016-09-29 05:30:24	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:   13s.  Last read position: chr1:21,664,944
INFO	2016-09-29 05:30:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:30:29	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    4s.  Last read position: chr1:37,867,118
INFO	2016-09-29 05:30:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:30:36	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    7s.  Last read position: chr1:52,799,423
INFO	2016-09-29 05:30:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:30:50	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:   14s.  Last read position: chr1:64,735,969
INFO	2016-09-29 05:30:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:30:57	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    6s.  Last read position: chr1:79,136,302
INFO	2016-09-29 05:30:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:30:59	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    2s.  Last read position: chr1:90,202,355
INFO	2016-09-29 05:30:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:02	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    3s.  Last read position: chr1:106,145,404
INFO	2016-09-29 05:31:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:06	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    4s.  Last read position: chr1:125,560,321
INFO	2016-09-29 05:31:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:09	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    2s.  Last read position: chr1:134,565,454
INFO	2016-09-29 05:31:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:12	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    3s.  Last read position: chr1:149,352,321
INFO	2016-09-29 05:31:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:18	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    6s.  Last read position: chr1:159,736,182
INFO	2016-09-29 05:31:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:22	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:    3s.  Last read position: chr1:170,385,601
INFO	2016-09-29 05:31:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:25	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    3s.  Last read position: chr1:180,221,218
INFO	2016-09-29 05:31:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:32	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:21s.  Time for last 1,000,000:    6s.  Last read position: chr1:189,884,451
INFO	2016-09-29 05:31:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:34	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    2s.  Last read position: chr2:7,102,439
INFO	2016-09-29 05:31:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:45	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:   10s.  Last read position: chr2:22,815,814
INFO	2016-09-29 05:31:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:47	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr2:30,094,316
INFO	2016-09-29 05:31:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:50	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    2s.  Last read position: chr2:36,132,512
INFO	2016-09-29 05:31:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:52	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    2s.  Last read position: chr2:51,235,194
INFO	2016-09-29 05:31:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:54	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    2s.  Last read position: chr2:66,103,466
INFO	2016-09-29 05:31:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:31:57	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    2s.  Last read position: chr2:76,403,906
INFO	2016-09-29 05:31:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:00	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    3s.  Last read position: chr2:91,645,013
INFO	2016-09-29 05:32:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:03	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    2s.  Last read position: chr2:98,667,220
INFO	2016-09-29 05:32:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:06	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    3s.  Last read position: chr2:112,489,493
INFO	2016-09-29 05:32:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:09	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    3s.  Last read position: chr2:122,284,602
INFO	2016-09-29 05:32:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:16	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:    6s.  Last read position: chr2:131,186,541
INFO	2016-09-29 05:32:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:18	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    2s.  Last read position: chr2:145,414,963
INFO	2016-09-29 05:32:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:23	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    5s.  Last read position: chr2:155,330,916
INFO	2016-09-29 05:32:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:26	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:15s.  Time for last 1,000,000:    3s.  Last read position: chr2:164,006,039
INFO	2016-09-29 05:32:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:31	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    4s.  Last read position: chr2:170,163,214
INFO	2016-09-29 05:32:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:39	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:28s.  Time for last 1,000,000:    8s.  Last read position: chr2:181,762,843
INFO	2016-09-29 05:32:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:42	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:30s.  Time for last 1,000,000:    2s.  Last read position: chr3:23,925,685
INFO	2016-09-29 05:32:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:45	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:34s.  Time for last 1,000,000:    3s.  Last read position: chr3:40,532,374
INFO	2016-09-29 05:32:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:49	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:38s.  Time for last 1,000,000:    3s.  Last read position: chr3:57,739,892
INFO	2016-09-29 05:32:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:55	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:    5s.  Last read position: chr3:73,847,050
INFO	2016-09-29 05:32:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:56	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:02:45s.  Time for last 1,000,000:    1s.  Last read position: chr3:87,781,925
INFO	2016-09-29 05:32:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:32:58	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:    2s.  Last read position: chr3:95,870,543
INFO	2016-09-29 05:32:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:01	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:02:49s.  Time for last 1,000,000:    2s.  Last read position: chr3:104,758,456
INFO	2016-09-29 05:33:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:02	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:02:51s.  Time for last 1,000,000:    1s.  Last read position: chr3:116,913,703
INFO	2016-09-29 05:33:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:06	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:02:55s.  Time for last 1,000,000:    3s.  Last read position: chr3:130,694,737
INFO	2016-09-29 05:33:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:08	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    1s.  Last read position: chr3:142,744,486
INFO	2016-09-29 05:33:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:11	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:02:59s.  Time for last 1,000,000:    2s.  Last read position: chr3:155,984,307
INFO	2016-09-29 05:33:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:13	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    2s.  Last read position: chr4:14,989,883
INFO	2016-09-29 05:33:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:16	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:05s.  Time for last 1,000,000:    3s.  Last read position: chr4:34,600,948
INFO	2016-09-29 05:33:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:23	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:12s.  Time for last 1,000,000:    6s.  Last read position: chr4:46,318,274
INFO	2016-09-29 05:33:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:30	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:19s.  Time for last 1,000,000:    7s.  Last read position: chr4:59,157,945
INFO	2016-09-29 05:33:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:32	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    2s.  Last read position: chr4:79,095,122
INFO	2016-09-29 05:33:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:36	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:    3s.  Last read position: chr4:96,140,889
INFO	2016-09-29 05:33:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:41	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:30s.  Time for last 1,000,000:    5s.  Last read position: chr4:108,277,083
INFO	2016-09-29 05:33:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:44	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:    3s.  Last read position: chr4:119,313,287
INFO	2016-09-29 05:33:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:49	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:03:38s.  Time for last 1,000,000:    4s.  Last read position: chr4:128,660,691
INFO	2016-09-29 05:33:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:51	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:03:40s.  Time for last 1,000,000:    1s.  Last read position: chr4:134,253,398
INFO	2016-09-29 05:33:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:53	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:03:42s.  Time for last 1,000,000:    2s.  Last read position: chr4:140,322,370
INFO	2016-09-29 05:33:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:55	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    2s.  Last read position: chr4:150,099,102
INFO	2016-09-29 05:33:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:33:57	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:    2s.  Last read position: chr5:5,559,748
INFO	2016-09-29 05:33:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:01	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:03:50s.  Time for last 1,000,000:    3s.  Last read position: chr5:24,578,720
INFO	2016-09-29 05:34:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:03	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:03:52s.  Time for last 1,000,000:    2s.  Last read position: chr5:34,413,477
INFO	2016-09-29 05:34:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:06	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:    2s.  Last read position: chr5:47,553,085
INFO	2016-09-29 05:34:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:09	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:03:58s.  Time for last 1,000,000:    3s.  Last read position: chr5:65,436,432
INFO	2016-09-29 05:34:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:12	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:01s.  Time for last 1,000,000:    3s.  Last read position: chr5:77,460,284
INFO	2016-09-29 05:34:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:21	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:    8s.  Last read position: chr5:97,543,760
INFO	2016-09-29 05:34:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:23	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    1s.  Last read position: chr5:108,012,503
INFO	2016-09-29 05:34:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:26	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:15s.  Time for last 1,000,000:    3s.  Last read position: chr5:115,885,123
INFO	2016-09-29 05:34:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:30	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    3s.  Last read position: chr5:123,135,379
INFO	2016-09-29 05:34:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:32	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    2s.  Last read position: chr5:133,062,790
INFO	2016-09-29 05:34:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:34	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:04:23s.  Time for last 1,000,000:    1s.  Last read position: chr5:140,191,258
INFO	2016-09-29 05:34:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:36	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:    1s.  Last read position: chr5:148,221,945
INFO	2016-09-29 05:34:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:38	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:    2s.  Last read position: chr6:14,207,612
INFO	2016-09-29 05:34:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:40	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:04:29s.  Time for last 1,000,000:    1s.  Last read position: chr6:30,826,515
INFO	2016-09-29 05:34:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:44	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:04:33s.  Time for last 1,000,000:    3s.  Last read position: chr6:43,038,818
INFO	2016-09-29 05:34:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:48	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    3s.  Last read position: chr6:54,700,233
INFO	2016-09-29 05:34:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:51	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:04:40s.  Time for last 1,000,000:    3s.  Last read position: chr6:72,114,153
INFO	2016-09-29 05:34:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:54	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:04:43s.  Time for last 1,000,000:    3s.  Last read position: chr6:86,524,185
INFO	2016-09-29 05:34:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:34:58	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:04:46s.  Time for last 1,000,000:    3s.  Last read position: chr6:96,526,405
INFO	2016-09-29 05:34:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:01	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:    3s.  Last read position: chr6:110,453,978
INFO	2016-09-29 05:35:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:13	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:02s.  Time for last 1,000,000:   12s.  Last read position: chr6:120,365,083
INFO	2016-09-29 05:35:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:16	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:04s.  Time for last 1,000,000:    2s.  Last read position: chr6:129,254,654
INFO	2016-09-29 05:35:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:19	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    2s.  Last read position: chr6:143,167,225
INFO	2016-09-29 05:35:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:24	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    5s.  Last read position: chr7:10,466,977
INFO	2016-09-29 05:35:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:27	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    3s.  Last read position: chr7:25,244,605
INFO	2016-09-29 05:35:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:31	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    3s.  Last read position: chr7:35,023,843
INFO	2016-09-29 05:35:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:35	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:05:24s.  Time for last 1,000,000:    3s.  Last read position: chr7:46,414,863
INFO	2016-09-29 05:35:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:40	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:05:29s.  Time for last 1,000,000:    5s.  Last read position: chr7:65,728,107
INFO	2016-09-29 05:35:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:43	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:05:32s.  Time for last 1,000,000:    2s.  Last read position: chr7:79,322,888
INFO	2016-09-29 05:35:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:45	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:05:34s.  Time for last 1,000,000:    2s.  Last read position: chr7:90,200,479
INFO	2016-09-29 05:35:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:47	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:05:36s.  Time for last 1,000,000:    2s.  Last read position: chr7:101,373,786
INFO	2016-09-29 05:35:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:50	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    2s.  Last read position: chr7:113,401,642
INFO	2016-09-29 05:35:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:52	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:05:41s.  Time for last 1,000,000:    2s.  Last read position: chr7:123,348,065
INFO	2016-09-29 05:35:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:56	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:05:45s.  Time for last 1,000,000:    4s.  Last read position: chr7:131,338,002
INFO	2016-09-29 05:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:35:58	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:05:47s.  Time for last 1,000,000:    2s.  Last read position: chr7:141,636,269
INFO	2016-09-29 05:35:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:07	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    8s.  Last read position: chr8:11,788,800
INFO	2016-09-29 05:36:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:09	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    2s.  Last read position: chr8:26,117,797
INFO	2016-09-29 05:36:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:12	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:06:01s.  Time for last 1,000,000:    2s.  Last read position: chr8:42,261,831
INFO	2016-09-29 05:36:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:17	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    5s.  Last read position: chr8:61,421,721
INFO	2016-09-29 05:36:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:21	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    3s.  Last read position: chr8:72,288,852
INFO	2016-09-29 05:36:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:24	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:06:13s.  Time for last 1,000,000:    3s.  Last read position: chr8:84,661,149
INFO	2016-09-29 05:36:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:29	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:06:18s.  Time for last 1,000,000:    4s.  Last read position: chr8:94,769,987
INFO	2016-09-29 05:36:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:31	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:06:20s.  Time for last 1,000,000:    2s.  Last read position: chr8:107,287,640
INFO	2016-09-29 05:36:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:33	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:06:22s.  Time for last 1,000,000:    2s.  Last read position: chr8:117,588,512
INFO	2016-09-29 05:36:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:36	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    2s.  Last read position: chr8:124,315,967
INFO	2016-09-29 05:36:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:38	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:06:27s.  Time for last 1,000,000:    2s.  Last read position: chr9:13,296,358
INFO	2016-09-29 05:36:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:41	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:    2s.  Last read position: chr9:25,562,326
INFO	2016-09-29 05:36:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:43	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:    2s.  Last read position: chr9:40,886,649
INFO	2016-09-29 05:36:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:48	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:06:37s.  Time for last 1,000,000:    4s.  Last read position: chr9:50,534,958
INFO	2016-09-29 05:36:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:50	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:06:39s.  Time for last 1,000,000:    2s.  Last read position: chr9:59,400,920
INFO	2016-09-29 05:36:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:36:53	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:06:42s.  Time for last 1,000,000:    3s.  Last read position: chr9:66,715,229
INFO	2016-09-29 05:36:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:01	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:06:50s.  Time for last 1,000,000:    8s.  Last read position: chr9:77,653,061
INFO	2016-09-29 05:37:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:05	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:06:54s.  Time for last 1,000,000:    4s.  Last read position: chr9:91,792,010
INFO	2016-09-29 05:37:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:09	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:06:58s.  Time for last 1,000,000:    3s.  Last read position: chr9:104,128,554
INFO	2016-09-29 05:37:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:13	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:07:02s.  Time for last 1,000,000:    3s.  Last read position: chr9:112,641,320
INFO	2016-09-29 05:37:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:17	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:07:06s.  Time for last 1,000,000:    3s.  Last read position: chr9:121,983,772
INFO	2016-09-29 05:37:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:20	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    3s.  Last read position: chr10:13,861,450
INFO	2016-09-29 05:37:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:25	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:07:14s.  Time for last 1,000,000:    4s.  Last read position: chr10:26,373,760
INFO	2016-09-29 05:37:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:27	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    2s.  Last read position: chr10:42,466,114
INFO	2016-09-29 05:37:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:30	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:    2s.  Last read position: chr10:57,744,122
INFO	2016-09-29 05:37:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:32	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:07:21s.  Time for last 1,000,000:    2s.  Last read position: chr10:67,568,537
INFO	2016-09-29 05:37:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:34	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:07:23s.  Time for last 1,000,000:    2s.  Last read position: chr10:78,194,494
INFO	2016-09-29 05:37:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:36	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:07:25s.  Time for last 1,000,000:    2s.  Last read position: chr10:84,317,220
INFO	2016-09-29 05:37:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:39	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    2s.  Last read position: chr10:94,944,253
INFO	2016-09-29 05:37:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:41	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:07:30s.  Time for last 1,000,000:    2s.  Last read position: chr10:110,255,953
INFO	2016-09-29 05:37:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:45	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    4s.  Last read position: chr10:121,314,725
INFO	2016-09-29 05:37:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:53	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:07:42s.  Time for last 1,000,000:    8s.  Last read position: chr11:3,328,572
INFO	2016-09-29 05:37:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:37:57	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:07:46s.  Time for last 1,000,000:    3s.  Last read position: chr11:16,161,336
INFO	2016-09-29 05:37:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:00	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:    3s.  Last read position: chr11:29,267,946
INFO	2016-09-29 05:38:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:03	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:07:52s.  Time for last 1,000,000:    3s.  Last read position: chr11:44,373,291
INFO	2016-09-29 05:38:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:06	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:    2s.  Last read position: chr11:53,326,957
INFO	2016-09-29 05:38:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:09	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    3s.  Last read position: chr11:61,381,582
INFO	2016-09-29 05:38:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:13	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:08:02s.  Time for last 1,000,000:    3s.  Last read position: chr11:70,039,329
INFO	2016-09-29 05:38:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:16	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:08:05s.  Time for last 1,000,000:    3s.  Last read position: chr11:77,521,958
INFO	2016-09-29 05:38:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:22	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:08:11s.  Time for last 1,000,000:    5s.  Last read position: chr11:84,819,563
INFO	2016-09-29 05:38:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:24	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    2s.  Last read position: chr11:94,525,445
INFO	2016-09-29 05:38:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:26	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:08:15s.  Time for last 1,000,000:    2s.  Last read position: chr11:100,319,536
INFO	2016-09-29 05:38:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:29	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    2s.  Last read position: chr11:106,318,974
INFO	2016-09-29 05:38:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:31	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:08:20s.  Time for last 1,000,000:    2s.  Last read position: chr11:115,319,943
INFO	2016-09-29 05:38:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:33	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:08:22s.  Time for last 1,000,000:    2s.  Last read position: chr11:120,252,871
INFO	2016-09-29 05:38:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:35	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:08:24s.  Time for last 1,000,000:    2s.  Last read position: chr12:14,340,915
INFO	2016-09-29 05:38:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:44	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    8s.  Last read position: chr12:33,305,146
INFO	2016-09-29 05:38:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:46	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    2s.  Last read position: chr12:52,603,684
INFO	2016-09-29 05:38:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:49	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:08:38s.  Time for last 1,000,000:    2s.  Last read position: chr12:69,751,002
INFO	2016-09-29 05:38:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:51	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:08:40s.  Time for last 1,000,000:    2s.  Last read position: chr12:80,004,842
INFO	2016-09-29 05:38:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:53	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:08:42s.  Time for last 1,000,000:    2s.  Last read position: chr12:88,643,548
INFO	2016-09-29 05:38:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:56	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    2s.  Last read position: chr12:102,460,081
INFO	2016-09-29 05:38:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:38:58	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:    2s.  Last read position: chr12:112,096,463
INFO	2016-09-29 05:38:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:00	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:08:49s.  Time for last 1,000,000:    2s.  Last read position: chr13:9,297,907
INFO	2016-09-29 05:39:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:02	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:08:51s.  Time for last 1,000,000:    2s.  Last read position: chr13:23,908,290
INFO	2016-09-29 05:39:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:05	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:08:54s.  Time for last 1,000,000:    2s.  Last read position: chr13:37,034,106
INFO	2016-09-29 05:39:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:07	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:08:56s.  Time for last 1,000,000:    2s.  Last read position: chr13:46,350,359
INFO	2016-09-29 05:39:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:11	MarkDuplicates	Read   148,000,000 records.  Elapsed time: 00:09:00s.  Time for last 1,000,000:    4s.  Last read position: chr13:55,426,524
INFO	2016-09-29 05:39:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:14	MarkDuplicates	Read   149,000,000 records.  Elapsed time: 00:09:02s.  Time for last 1,000,000:    2s.  Last read position: chr13:69,610,853
INFO	2016-09-29 05:39:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:17	MarkDuplicates	Read   150,000,000 records.  Elapsed time: 00:09:06s.  Time for last 1,000,000:    3s.  Last read position: chr13:85,197,828
INFO	2016-09-29 05:39:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:20	MarkDuplicates	Read   151,000,000 records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:    3s.  Last read position: chr13:98,648,278
INFO	2016-09-29 05:39:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:29	MarkDuplicates	Read   152,000,000 records.  Elapsed time: 00:09:18s.  Time for last 1,000,000:    8s.  Last read position: chr13:110,177,949
INFO	2016-09-29 05:39:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:32	MarkDuplicates	Read   153,000,000 records.  Elapsed time: 00:09:21s.  Time for last 1,000,000:    3s.  Last read position: chr14:10,779,613
INFO	2016-09-29 05:39:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:36	MarkDuplicates	Read   154,000,000 records.  Elapsed time: 00:09:25s.  Time for last 1,000,000:    3s.  Last read position: chr14:25,535,524
INFO	2016-09-29 05:39:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:39	MarkDuplicates	Read   155,000,000 records.  Elapsed time: 00:09:27s.  Time for last 1,000,000:    2s.  Last read position: chr14:36,931,931
INFO	2016-09-29 05:39:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:42	MarkDuplicates	Read   156,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:    3s.  Last read position: chr14:54,697,148
INFO	2016-09-29 05:39:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:44	MarkDuplicates	Read   157,000,000 records.  Elapsed time: 00:09:33s.  Time for last 1,000,000:    2s.  Last read position: chr14:64,218,338
INFO	2016-09-29 05:39:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:48	MarkDuplicates	Read   158,000,000 records.  Elapsed time: 00:09:36s.  Time for last 1,000,000:    3s.  Last read position: chr14:74,906,081
INFO	2016-09-29 05:39:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:52	MarkDuplicates	Read   159,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    4s.  Last read position: chr14:90,715,088
INFO	2016-09-29 05:39:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:54	MarkDuplicates	Read   160,000,000 records.  Elapsed time: 00:09:43s.  Time for last 1,000,000:    2s.  Last read position: chr14:108,712,011
INFO	2016-09-29 05:39:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:57	MarkDuplicates	Read   161,000,000 records.  Elapsed time: 00:09:46s.  Time for last 1,000,000:    2s.  Last read position: chr14:124,234,017
INFO	2016-09-29 05:39:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:39:59	MarkDuplicates	Read   162,000,000 records.  Elapsed time: 00:09:48s.  Time for last 1,000,000:    2s.  Last read position: chr15:23,596,033
INFO	2016-09-29 05:39:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:01	MarkDuplicates	Read   163,000,000 records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:    2s.  Last read position: chr15:38,606,583
INFO	2016-09-29 05:40:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:03	MarkDuplicates	Read   164,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:    2s.  Last read position: chr15:58,851,637
INFO	2016-09-29 05:40:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:05	MarkDuplicates	Read   165,000,000 records.  Elapsed time: 00:09:54s.  Time for last 1,000,000:    2s.  Last read position: chr15:72,808,333
INFO	2016-09-29 05:40:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:08	MarkDuplicates	Read   166,000,000 records.  Elapsed time: 00:09:57s.  Time for last 1,000,000:    2s.  Last read position: chr15:79,625,280
INFO	2016-09-29 05:40:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:16	MarkDuplicates	Read   167,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:    8s.  Last read position: chr15:85,896,516
INFO	2016-09-29 05:40:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:18	MarkDuplicates	Read   168,000,000 records.  Elapsed time: 00:10:07s.  Time for last 1,000,000:    2s.  Last read position: chr15:97,684,547
INFO	2016-09-29 05:40:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:20	MarkDuplicates	Read   169,000,000 records.  Elapsed time: 00:10:09s.  Time for last 1,000,000:    2s.  Last read position: chr15:103,476,139
INFO	2016-09-29 05:40:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:24	MarkDuplicates	Read   170,000,000 records.  Elapsed time: 00:10:12s.  Time for last 1,000,000:    3s.  Last read position: chr16:14,161,975
INFO	2016-09-29 05:40:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:26	MarkDuplicates	Read   171,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    2s.  Last read position: chr16:24,196,328
INFO	2016-09-29 05:40:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:28	MarkDuplicates	Read   172,000,000 records.  Elapsed time: 00:10:17s.  Time for last 1,000,000:    2s.  Last read position: chr16:34,452,137
INFO	2016-09-29 05:40:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:30	MarkDuplicates	Read   173,000,000 records.  Elapsed time: 00:10:19s.  Time for last 1,000,000:    2s.  Last read position: chr16:47,033,299
INFO	2016-09-29 05:40:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:32	MarkDuplicates	Read   174,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:    2s.  Last read position: chr16:62,786,509
INFO	2016-09-29 05:40:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:35	MarkDuplicates	Read   175,000,000 records.  Elapsed time: 00:10:24s.  Time for last 1,000,000:    2s.  Last read position: chr16:84,072,806
INFO	2016-09-29 05:40:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:37	MarkDuplicates	Read   176,000,000 records.  Elapsed time: 00:10:26s.  Time for last 1,000,000:    2s.  Last read position: chr16:94,568,012
INFO	2016-09-29 05:40:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:39	MarkDuplicates	Read   177,000,000 records.  Elapsed time: 00:10:28s.  Time for last 1,000,000:    2s.  Last read position: chr17:10,858,709
INFO	2016-09-29 05:40:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:42	MarkDuplicates	Read   178,000,000 records.  Elapsed time: 00:10:30s.  Time for last 1,000,000:    2s.  Last read position: chr17:25,192,100
INFO	2016-09-29 05:40:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:44	MarkDuplicates	Read   179,000,000 records.  Elapsed time: 00:10:33s.  Time for last 1,000,000:    2s.  Last read position: chr17:30,852,674
INFO	2016-09-29 05:40:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:46	MarkDuplicates	Read   180,000,000 records.  Elapsed time: 00:10:35s.  Time for last 1,000,000:    2s.  Last read position: chr17:36,274,579
INFO	2016-09-29 05:40:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:51	MarkDuplicates	Read   181,000,000 records.  Elapsed time: 00:10:40s.  Time for last 1,000,000:    4s.  Last read position: chr17:46,535,625
INFO	2016-09-29 05:40:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:40:59	MarkDuplicates	Read   182,000,000 records.  Elapsed time: 00:10:48s.  Time for last 1,000,000:    8s.  Last read position: chr17:56,626,315
INFO	2016-09-29 05:40:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:02	MarkDuplicates	Read   183,000,000 records.  Elapsed time: 00:10:51s.  Time for last 1,000,000:    2s.  Last read position: chr17:71,179,061
INFO	2016-09-29 05:41:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:04	MarkDuplicates	Read   184,000,000 records.  Elapsed time: 00:10:53s.  Time for last 1,000,000:    2s.  Last read position: chr17:83,094,989
INFO	2016-09-29 05:41:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:07	MarkDuplicates	Read   185,000,000 records.  Elapsed time: 00:10:56s.  Time for last 1,000,000:    3s.  Last read position: chr17:94,205,427
INFO	2016-09-29 05:41:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:10	MarkDuplicates	Read   186,000,000 records.  Elapsed time: 00:10:59s.  Time for last 1,000,000:    2s.  Last read position: chr18:20,258,396
INFO	2016-09-29 05:41:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:12	MarkDuplicates	Read   187,000,000 records.  Elapsed time: 00:11:01s.  Time for last 1,000,000:    2s.  Last read position: chr18:35,201,437
INFO	2016-09-29 05:41:12	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:16	MarkDuplicates	Read   188,000,000 records.  Elapsed time: 00:11:05s.  Time for last 1,000,000:    3s.  Last read position: chr18:47,348,076
INFO	2016-09-29 05:41:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:20	MarkDuplicates	Read   189,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    3s.  Last read position: chr18:61,176,957
INFO	2016-09-29 05:41:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:22	MarkDuplicates	Read   190,000,000 records.  Elapsed time: 00:11:11s.  Time for last 1,000,000:    2s.  Last read position: chr18:72,780,942
INFO	2016-09-29 05:41:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:26	MarkDuplicates	Read   191,000,000 records.  Elapsed time: 00:11:14s.  Time for last 1,000,000:    3s.  Last read position: chr18:82,942,858
INFO	2016-09-29 05:41:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:29	MarkDuplicates	Read   192,000,000 records.  Elapsed time: 00:11:18s.  Time for last 1,000,000:    3s.  Last read position: chr19:6,975,055
INFO	2016-09-29 05:41:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:35	MarkDuplicates	Read   193,000,000 records.  Elapsed time: 00:11:23s.  Time for last 1,000,000:    5s.  Last read position: chr19:17,764,565
INFO	2016-09-29 05:41:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:37	MarkDuplicates	Read   194,000,000 records.  Elapsed time: 00:11:26s.  Time for last 1,000,000:    2s.  Last read position: chr19:32,018,971
INFO	2016-09-29 05:41:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:40	MarkDuplicates	Read   195,000,000 records.  Elapsed time: 00:11:28s.  Time for last 1,000,000:    2s.  Last read position: chr19:42,168,012
INFO	2016-09-29 05:41:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:42	MarkDuplicates	Read   196,000,000 records.  Elapsed time: 00:11:31s.  Time for last 1,000,000:    2s.  Last read position: chr19:52,163,760
INFO	2016-09-29 05:41:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:50	MarkDuplicates	Read   197,000,000 records.  Elapsed time: 00:11:39s.  Time for last 1,000,000:    8s.  Last read position: chrX:7,901,616
INFO	2016-09-29 05:41:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:53	MarkDuplicates	Read   198,000,000 records.  Elapsed time: 00:11:42s.  Time for last 1,000,000:    2s.  Last read position: chrX:51,473,736
INFO	2016-09-29 05:41:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:55	MarkDuplicates	Read   199,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    2s.  Last read position: chrX:95,030,923
INFO	2016-09-29 05:41:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:57	MarkDuplicates	Read   200,000,000 records.  Elapsed time: 00:11:46s.  Time for last 1,000,000:    2s.  Last read position: chrX:134,963,546
INFO	2016-09-29 05:41:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:41:59	MarkDuplicates	Read   201,000,000 records.  Elapsed time: 00:11:48s.  Time for last 1,000,000:    2s.  Last read position: chrX:167,192,814
INFO	2016-09-29 05:41:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 05:42:00	MarkDuplicates	Read 201420018 records. 0 pairs never matched.
INFO	2016-09-29 05:42:02	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2762246608; totalMemory: 2850095104; maxMemory: 3817799680
INFO	2016-09-29 05:42:02	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-29 05:42:02	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-29 05:42:02	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-29 05:42:58	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-29 05:43:02	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2827021016; totalMemory: 2854486016; maxMemory: 3817799680
INFO	2016-09-29 05:43:02	MarkDuplicates	Marking 159965683 records as duplicates.
INFO	2016-09-29 05:43:02	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-29 05:44:46	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:44s.  Time for last 10,000,000:  104s.  Last read position: chr1:149,352,321
INFO	2016-09-29 05:46:29	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:27s.  Time for last 10,000,000:  103s.  Last read position: chr2:66,103,466
INFO	2016-09-29 05:48:15	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:05:13s.  Time for last 10,000,000:  105s.  Last read position: chr2:170,163,214
INFO	2016-09-29 05:49:59	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:06:57s.  Time for last 10,000,000:  103s.  Last read position: chr3:130,694,737
INFO	2016-09-29 05:51:43	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:08:41s.  Time for last 10,000,000:  104s.  Last read position: chr4:119,313,287
INFO	2016-09-29 05:53:28	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:10:26s.  Time for last 10,000,000:  105s.  Last read position: chr5:77,460,284
INFO	2016-09-29 05:55:13	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:12:11s.  Time for last 10,000,000:  104s.  Last read position: chr6:43,038,818
INFO	2016-09-29 05:56:57	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:13:55s.  Time for last 10,000,000:  103s.  Last read position: chr7:25,244,605
INFO	2016-09-29 05:58:41	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:15:39s.  Time for last 10,000,000:  103s.  Last read position: chr7:141,636,269
INFO	2016-09-29 06:00:24	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:17:22s.  Time for last 10,000,000:  103s.  Last read position: chr8:124,315,967
INFO	2016-09-29 06:02:06	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:19:04s.  Time for last 10,000,000:  101s.  Last read position: chr9:112,641,320
INFO	2016-09-29 06:03:50	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:20:48s.  Time for last 10,000,000:  103s.  Last read position: chr10:110,255,953
INFO	2016-09-29 06:05:34	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:22:31s.  Time for last 10,000,000:  103s.  Last read position: chr11:84,819,563
INFO	2016-09-29 06:07:31	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:24:29s.  Time for last 10,000,000:  117s.  Last read position: chr12:80,004,842
INFO	2016-09-29 06:09:34	MarkDuplicates	Written   150,000,000 records.  Elapsed time: 00:26:32s.  Time for last 10,000,000:  122s.  Last read position: chr13:85,197,828
INFO	2016-09-29 06:11:29	MarkDuplicates	Written   160,000,000 records.  Elapsed time: 00:28:27s.  Time for last 10,000,000:  115s.  Last read position: chr14:108,712,011
INFO	2016-09-29 06:13:30	MarkDuplicates	Written   170,000,000 records.  Elapsed time: 00:30:28s.  Time for last 10,000,000:  121s.  Last read position: chr16:14,161,975
INFO	2016-09-29 06:15:30	MarkDuplicates	Written   180,000,000 records.  Elapsed time: 00:32:28s.  Time for last 10,000,000:  119s.  Last read position: chr17:36,274,579
INFO	2016-09-29 06:17:31	MarkDuplicates	Written   190,000,000 records.  Elapsed time: 00:34:29s.  Time for last 10,000,000:  121s.  Last read position: chr18:72,780,942
INFO	2016-09-29 06:19:18	MarkDuplicates	Written   200,000,000 records.  Elapsed time: 00:36:16s.  Time for last 10,000,000:  106s.  Last read position: chrX:134,963,546
Could not delete file /tmp/imk1/sortingcollection.7959922847880466682.tmp
Could not delete file /tmp/imk1/sortingcollection.555744465734370765.tmp
INFO	2016-09-29 06:19:33	MarkDuplicates	Before output close freeMemory: 2318137288; totalMemory: 2335178752; maxMemory: 3817799680
INFO	2016-09-29 06:19:34	MarkDuplicates	After output close freeMemory: 2318136704; totalMemory: 2335178752; maxMemory: 3817799680
[Thu Sep 29 06:19:34 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 49.44 minutes.
Runtime.totalMemory()=2335178752

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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/ZF7/out/qc/rep1/ZF7_allReps.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--------------------
19024 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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--------------------
6573 (process ID) old priority 0, new priority 10


 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.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--------------------
6651 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.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/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr2/ZF7_allReps.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/pseudo_reps/rep1/pr1/ZF7_allReps.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--------------------
9447 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH

 

 
# 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/ZF7/out/align/rep1/ZF7_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc

# SYS command. line 222

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 

   
--------------------Stdout--------------------
22275 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 4 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/qc/rep1/ZF7_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9794.1.q/RtmpRxXB0i/ZF7_allReps.nodup.15M.tagAlign57453692a235
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1994709 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.217383198646285,0.208662511853117,0.207085165136283 
Top 3 estimates for fragment length 160,315,425 
Window half size 570 
Phantom peak location 55 
Phantom peak Correlation 0.2107381 
Normalized Strand cross-correlation coefficient (NSC) 1.089799 
Relative Strand Cross correlation Coefficient (RSC) 1.589768 
Phantom Peak Quality Tag 2 
null device 
          1 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools

 

 
# SYS command. line 56

 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 59

 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 63

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 79

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 

 
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
  
--------------------Stdout--------------------
10080 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/peak/spp/rep1/ZF7_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/rep1/ZF7_allReps.nodup.tagAlign.gz 
opened /tmp/9798.1.q/RtmpqsQwwF/ZF7_allReps.nodup.tagAlign27a2527e0297
done. read 41454335 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF7/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9798.1.q/RtmpqsQwwF/mousePrimaryBCellInput.nodup.tagAlign27a2292ecb44
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.3990269 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.43484250254046 
Top 3 estimates for fragment length 160 
Window half size 565 
Phantom peak location 55 
Phantom peak Correlation 0.4216947 
Normalized Strand cross-correlation coefficient (NSC) 1.089757 
Relative Strand Cross correlation Coefficient (RSC) 1.580021 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.4104313  
 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools