spp rep1

 chipseq.bds.20160928_164730_405/task.callpeak_spp.spp_rep1.line_54.id_25
 

 chipseq.bds.20160928_164730_405_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10
chipseq.bds.20160928_164730_405_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20160928_164730_405_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 chipseq.bds.20160928_164730_405_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11
chipseq.bds.20160928_164730_405_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20160928_164730_405_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
chipseq.bds.20160928_164730_405_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
chipseq.bds.20160928_164730_405_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
chipseq.bds.20160928_164730_405_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
 

 
# 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/ZF4/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--------------------
2766 (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... 21.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 22.72 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... 24.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.06 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... 25.81 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.80 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.99 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.09 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.30 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.55 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.34 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.24 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.76 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... 23.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.36 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... 25.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.58 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... 23.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.35 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... 23.95 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... 26.03 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.97 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... 25.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.19 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... 25.17 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.57 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.30 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... 25.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.89 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... 24.30 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... 23.49 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... 21.15 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.70 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.86 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... 20.63 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... 23.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.85 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... 20.28 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... 20.33 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... 20.10 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... 20.09 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... 20.22 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... 20.01 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... 20.06 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... 20.22 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... 20.04 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... 5.52 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: 2190.493 sec; CPU: 2190.176 sec

 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF4_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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--------------------
11680 (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] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 189.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 191.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.04 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 218.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.00 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 186.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 203.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 221.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 213.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 186.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 206.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.11 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.37 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 230.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 219.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 213.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 211.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 198.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.57 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... 176.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.32 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.23 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.14 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... 30.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.61 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.01 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 192.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 216.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 217.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 209.72 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 211.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 212.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 191.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.85 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... 161.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.23 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.9% 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] 81264640 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.87 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.81 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 90963968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.38 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.74 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.44 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 23.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.75 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... 168.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 100139008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.59 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 208.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.23 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 149.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.19 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.82 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 26.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 216.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 215.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 206.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 219.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 209.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.22 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 208.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 220.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 214.17 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 216.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 217.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 191.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.62 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.37 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 208.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 191.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 189.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.48 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 142.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.48 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.19 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 174.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 186.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.96 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 189.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.76 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 186.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 168.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 167.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.11 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... 171.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.30 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 180.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.84 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.14 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 198.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 203.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 206.50 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 165937152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 205.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 192.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 164.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 156.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 146.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 145.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 166.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 132.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 169.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.14 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.67 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 150.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 143.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.45 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 136.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 148.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 151.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.37 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 147.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 144.70 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 173.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 135.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 161.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.29 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.43 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.82 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 141.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 140.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 182714368 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 134.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.36 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.30 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 130.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.88 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.07 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 133.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 139.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 137.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.20 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 126.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.28 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.69 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 128.97 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 124.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.64 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 18.91 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 22.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 24.68 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 25.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 20.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 21.94 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.96 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 1.5% 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] 196083712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.72 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 197656576 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... 0.03 sec
[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.54 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.95 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.41 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.58 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.94 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 202113024 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.41 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.71 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.49 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.1% 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] 208666624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.09 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 208928768 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... 0.07 sec
[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.73 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.25 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 75.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 63.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.25 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.76 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.16 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 216793088 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... 0.04 sec
[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.66 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.47 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.88 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.31 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.00 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.99 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 76.53 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 70.39 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 69.44 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... 65.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 66.86 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... 71.14 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... 69.27 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 71.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 68.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 229638144 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.32 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... 123.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.40 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.39 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.49 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.46 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 127.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.05 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.05 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... 112.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 238288896 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.59 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238551040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 131.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 129.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 123.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 121.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.65 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.29 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 122.60 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 108.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 125.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 244842496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 245366784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.67 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... 113.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.74 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 119.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 118.31 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 247726080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 117.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 247988224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 116.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.42 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.19 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 249298944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.56 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 95.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 249823232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 250347520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 250609664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 250871808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 251133952 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 251396096 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 251658240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 251920384 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.58 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 252182528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 252444672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 252706816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 252968960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 253231104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 253493248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 253755392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 90.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 254017536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 254279680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 254541824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.19 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 254803968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.04 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 255066112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.66 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 255328256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 255590400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 255852544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 256114688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.82 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 256376832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 256638976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 256901120 sequences have been processed.
[bwa_read_seq] 1.1% 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] 257163264 sequences have been processed.
[bwa_read_seq] 1.1% 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] 257425408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 257687552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 257949696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.98 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 258211840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 258473984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 258736128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 258998272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 259260416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 259522560 sequences have been processed.
[bwa_read_seq] 1.2% 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] 259784704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 260046848 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... 0.06 sec
[bwa_aln_core] 260308992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 94.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 260571136 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 260833280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 261095424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 101.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 261357568 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.07 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 261619712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 261881856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262406144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.70 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262668288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 262930432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 263192576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 263454720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.92 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 263716864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 263979008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 264241152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.68 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 264503296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 264765440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 96.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 265027584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 265289728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 265551872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 265814016 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 266076160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 266338304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 266600448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 266862592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 267124736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 93.09 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 267386880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 267649024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 267911168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 268173312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 268435456 sequences have been processed.
[bwa_read_seq] 1.1% 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] 268697600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 268959744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 269221888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 269484032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 269746176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 83.96 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 270008320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 270270464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.61 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 270532608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 270794752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 87.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 271056896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 91.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 271319040 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] 271581184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 271843328 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.75 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 272105472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 272367616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 272629760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 272891904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 273154048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 273416192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 102.49 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 273678336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 273940480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.60 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 274202624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 89.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 274464768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 92.69 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 274726912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 85.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 274989056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 81.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 275251200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 79.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 275513344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 80.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 275775488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 78.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 276037632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 276299776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 276561920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 276824064 sequences have been processed.
[bwa_read_seq] 1.1% 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] 277086208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 277348352 sequences have been processed.
[bwa_read_seq] 1.2% 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] 277610496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.56 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 277872640 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 278134784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 82.85 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 278396928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 84.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 278659072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 86.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 278921216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 88.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 279183360 sequences have been processed.
[bwa_read_seq] 16.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 0.05 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 279183439 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/ZF4_allReps.fastq.gz
[main] Real time: 41806.402 sec; CPU: 144603.738 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/ZF4/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/ZF4/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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--------------------
17630 (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... 34.96 sec
[bwa_aln_core] refine gapped alignments... 10.69 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.66 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.37 sec
[bwa_aln_core] refine gapped alignments... 6.19 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.35 sec
[bwa_aln_core] refine gapped alignments... 8.05 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.02 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.50 sec
[bwa_aln_core] refine gapped alignments... 10.21 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.79 sec
[bwa_aln_core] refine gapped alignments... 9.79 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.34 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.40 sec
[bwa_aln_core] refine gapped alignments... 10.80 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.25 sec
[bwa_aln_core] refine gapped alignments... 1.11 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.64 sec
[bwa_aln_core] refine gapped alignments... 0.84 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.99 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.85 sec
[bwa_aln_core] refine gapped alignments... 3.93 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.64 sec
[bwa_aln_core] refine gapped alignments... 9.05 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.89 sec
[bwa_aln_core] refine gapped alignments... 0.88 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.86 sec
[bwa_aln_core] refine gapped alignments... 1.12 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.50 sec
[bwa_aln_core] refine gapped alignments... 0.73 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.64 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.28 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.08 sec
[bwa_aln_core] refine gapped alignments... 5.63 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.97 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.51 sec
[bwa_aln_core] refine gapped alignments... 8.75 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.01 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.90 sec
[bwa_aln_core] refine gapped alignments... 0.94 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.94 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.89 sec
[bwa_aln_core] refine gapped alignments... 2.82 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.97 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 68.60 sec
[bwa_aln_core] refine gapped alignments... 5.31 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 79.91 sec
[bwa_aln_core] refine gapped alignments... 6.97 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.97 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.14 sec
[bwa_aln_core] refine gapped alignments... 4.45 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.46 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 52.92 sec
[bwa_aln_core] refine gapped alignments... 3.40 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... 57.97 sec
[bwa_aln_core] refine gapped alignments... 9.60 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.19 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.53 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.05 sec
[bwa_aln_core] refine gapped alignments... 15.67 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.60 sec
[bwa_aln_core] refine gapped alignments... 15.88 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.53 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.26 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.85 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.45 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.65 sec
[bwa_aln_core] refine gapped alignments... 6.47 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.46 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.86 sec
[bwa_aln_core] refine gapped alignments... 3.63 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.50 sec
[bwa_aln_core] refine gapped alignments... 6.98 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.29 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 69.85 sec
[bwa_aln_core] refine gapped alignments... 9.42 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 83.87 sec
[bwa_aln_core] refine gapped alignments... 12.07 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... 87.31 sec
[bwa_aln_core] refine gapped alignments... 11.08 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 60.35 sec
[bwa_aln_core] refine gapped alignments... 5.52 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 85.28 sec
[bwa_aln_core] refine gapped alignments... 15.64 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.79 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.60 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.63 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... 0.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.24 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17825792 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... 0.47 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.64 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.89 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.12 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.55 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.71 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 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... 40.47 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 56.58 sec
[bwa_aln_core] refine gapped alignments... 4.31 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 75.97 sec
[bwa_aln_core] refine gapped alignments... 8.61 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 70.02 sec
[bwa_aln_core] refine gapped alignments... 3.92 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.11 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.20 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.47 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.29 sec
[bwa_aln_core] refine gapped alignments... 1.23 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.28 sec
[bwa_aln_core] refine gapped alignments... 2.18 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.56 sec
[bwa_aln_core] refine gapped alignments... 4.76 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.48 sec
[bwa_aln_core] refine gapped alignments... 8.66 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... 69.17 sec
[bwa_aln_core] refine gapped alignments... 6.29 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.52 sec
[bwa_aln_core] refine gapped alignments... 10.25 sec
[bwa_aln_core] print alignments... 0.15 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/ZF4/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 3585.823 sec; CPU: 3463.355 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/ZF4/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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/ZF4/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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--------------------
16453 (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/ZF4/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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/ZF4/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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--------------------
16983 (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 18:35:28 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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 18:35:28 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 18:35:28	MarkDuplicates	Start of doWork freeMemory: 255390112; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 18:35:28	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 18:35:28	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 18:35:37	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:08s.  Time for last 1,000,000:    8s.  Last read position: chr1:174,151,470
INFO	2016-09-28 18:35:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:35:42	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    5s.  Last read position: chr2:135,780,411
INFO	2016-09-28 18:35:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:35:47	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    4s.  Last read position: chr3:122,530,375
INFO	2016-09-28 18:35:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:35:50	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    3s.  Last read position: chr4:135,044,888
INFO	2016-09-28 18:35:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:35:56	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    5s.  Last read position: chr5:135,067,778
INFO	2016-09-28 18:35:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:35:58	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    2s.  Last read position: chr6:144,681,933
INFO	2016-09-28 18:35:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:01	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    2s.  Last read position: chr8:12,749,386
INFO	2016-09-28 18:36:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:05	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:    3s.  Last read position: chr9:42,425,131
INFO	2016-09-28 18:36:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:07	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:38s.  Time for last 1,000,000:    2s.  Last read position: chr10:69,658,983
INFO	2016-09-28 18:36:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:10	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    2s.  Last read position: chr11:86,536,377
INFO	2016-09-28 18:36:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    4s.  Last read position: chr13:6,026,344
INFO	2016-09-28 18:36:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:16	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:46s.  Time for last 1,000,000:    1s.  Last read position: chr14:54,434,282
INFO	2016-09-28 18:36:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:19	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    3s.  Last read position: chr15:98,839,731
INFO	2016-09-28 18:36:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:23	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    3s.  Last read position: chr17:62,456,013
INFO	2016-09-28 18:36:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:25	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    2s.  Last read position: chr19:38,585,732
INFO	2016-09-28 18:36:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 18:36:33	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 18:36:34	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2444291104; totalMemory: 2530869248; maxMemory: 3817799680
INFO	2016-09-28 18:36:34	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 18:36:34	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 18:36:34	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 18:36:38	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 18:36:38	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1944927464; totalMemory: 2921070592; maxMemory: 3817799680
INFO	2016-09-28 18:36:38	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 18:36:38	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 18:37:58	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:19s.  Time for last 10,000,000:   79s.  Last read position: chr11:86,536,377
INFO	2016-09-28 18:38:41	MarkDuplicates	Before output close freeMemory: 2892593288; totalMemory: 2920677376; maxMemory: 3817799680
INFO	2016-09-28 18:38:42	MarkDuplicates	After output close freeMemory: 2920904000; totalMemory: 2948988928; maxMemory: 3817799680
[Wed Sep 28 18:38:42 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.24 minutes.
Runtime.totalMemory()=2948988928

 

 
# 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/ZF4/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/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/ZF4/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--------------------
17411 (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/ZF4/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/ZF4/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--------------------
17856 (process ID) old priority 0, new priority 10

Waiting for 26 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/ZF4/out/align/rep1/ZF4_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF4_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_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--------------------
5992 (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] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.91 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.43 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.47 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.59 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.40 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.30 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.69 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.66 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.03 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.18 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 3145728 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... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.24 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.14 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.99 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.81 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.79 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.42 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.58 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.24 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.30 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.38 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.84 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.83 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.55 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.24 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.54 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.20 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.03 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.32 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.15 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.38 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.08 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.88 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.45 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.64 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.23 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.09 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.55 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.36 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.61 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.74 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.17 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.93 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.78 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.73 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.73 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.66 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.97 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.50 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.73 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.49 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.86 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.92 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.47 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.83 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.81 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.79 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.65 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.85 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.50 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.50 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.79 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.94 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.03 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.12 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.58 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.92 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.90 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.81 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.27 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.60 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.13 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.11 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.69 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.73 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.88 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.60 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.11 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.78 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.95 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.22 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.69 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.67 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.76 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.61 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.26 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.78 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.95 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.45 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.00 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.43 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.55 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.52 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.15 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.74 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.04 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.51 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.39 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.83 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.40 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.60 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.86 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.02 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.31 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.67 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.07 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.86 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.52 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.78 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.07 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.23 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.61 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.34 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.86 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.48 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.52 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.77 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.83 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.68 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.77 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.44 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.63 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.38 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.98 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.12 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.56 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.27 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.49 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.65 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.13 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.38 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.64 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.70 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.15 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.88 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.91 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.32 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.30 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.77 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.74 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.92 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.80 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.23 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.20 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.55 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.66 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.29 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.59 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.45 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.23 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.46 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.17 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.74 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.02 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.81 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.64 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.64 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.65 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.40 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.85 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.23 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.36 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.54 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.69 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.20 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.14 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.97 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.27 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.30 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.94 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.07 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.41 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.36 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.70 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.42 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.00 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.67 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.58 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.74 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.39 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.12 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.15 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.98 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.77 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.18 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.32 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.86 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.71 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.13 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.52 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.58 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.27 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.31 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.06 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.19 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.07 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.65 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.33 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.34 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.21 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.61 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.66 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.43 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.16 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.52 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.74 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.56 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.53 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.57 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.68 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.21 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.10 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 74186752 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... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.26 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 4.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.95 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.82 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.51 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.96 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.32 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.35 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.17 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.44 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.18 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.50 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.47 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.60 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 88080384 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 88342528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.19 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 88604672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.74 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 88866816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 89128960 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.70 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 89391104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 89653248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.59 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 89915392 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 90177536 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 90439680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 90701824 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.56 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 90963968 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... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 91226112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 91488256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.81 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 91750400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.89 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 92012544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.65 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 92274688 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 92536832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.60 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 92798976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.95 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 93061120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 93323264 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.75 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 93585408 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 93847552 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 94109696 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 94371840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 94633984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.04 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 94896128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 95158272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 95420416 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.93 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 95682560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.88 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 95944704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.92 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 96206848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.10 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 96468992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 96731136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.33 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 96993280 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 97255424 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.26 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 97517568 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.06 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 97779712 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.05 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 98041856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.13 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 98304000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.03 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 98566144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.94 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 98828288 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.86 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 99090432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.99 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 99352576 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 99614720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 99876864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.08 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 100139008 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... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 100401152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 100663296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 100925440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 101187584 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 101449728 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 101711872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 101974016 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 102236160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 102498304 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 102760448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 103022592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 103284736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 103546880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 103809024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 104071168 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 104333312 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 104595456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.22 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 104857600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 105119744 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 105381888 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 105644032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 105906176 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 106168320 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 106430464 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 106692608 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 106954752 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 107216896 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 107479040 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.27 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 107741184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 108003328 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 108265472 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 108527616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 108789760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 109051904 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.23 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 109314048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 109576192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 109838336 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 110100480 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 110362624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 110624768 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 110886912 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 111149056 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 111411200 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 111673344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 111935488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 112197632 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 112459776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 112721920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 112984064 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 113246208 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 113508352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 113770496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 114032640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 114294784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 114556928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.25 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 114819072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 115081216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 115343360 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 115605504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 115867648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 116129792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.24 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 116391936 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 116654080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 116916224 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 117178368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 117440512 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 117702656 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 117964800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 118226944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 118489088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 118751232 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.26 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 119013376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 119275520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 119537664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 119799808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.31 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 120061952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 120324096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 120586240 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 120848384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 121110528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 121372672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.35 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 121634816 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 121896960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 122159104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 122421248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 122683392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 122945536 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 123207680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 123469824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 123731968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 123994112 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 124256256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 124518400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.28 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 124780544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 125042688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 125304832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 125566976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.29 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 125829120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 126091264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 126353408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.63 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 126615552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.37 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 126877696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.33 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 127139840 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 127401984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.30 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 127664128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 127926272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.36 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 128188416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 128450560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 128712704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 128974848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 129236992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.45 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 129499136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 129761280 sequences have been processed.
[bwa_read_seq] 2.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 130023424 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.43 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 130285568 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 130547712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 130809856 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.34 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 131072000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.32 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 131334144 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 131596288 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.46 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 131858432 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 132120576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 132382720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 132644864 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.38 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 132907008 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 133169152 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.44 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 133431296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 133693440 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.49 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 133955584 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.39 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 134217728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.41 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 134479872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 134742016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 135004160 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 135266304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 135528448 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 135790592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.50 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 136052736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.42 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 136314880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.47 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 136577024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 136839168 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 137101312 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 137363456 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 137625600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 137887744 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.58 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 138149888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.60 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 138412032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.59 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 138674176 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.48 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 138936320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 139198464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 139460608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.51 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 139722752 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 139984896 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.62 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 140247040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 140509184 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.61 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 140771328 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 141033472 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.52 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 141295616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 141557760 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.54 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 141819904 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.65 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 142082048 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 142344192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.71 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 142606336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 0.33 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 142868480 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.66 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 143130624 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 143392768 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.43 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 143654912 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.20 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 143917056 sequences have been processed.
[bwa_read_seq] 2.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.19 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 144179200 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.06 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 144441344 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.15 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 144703488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.99 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 144965632 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.20 sec
[bwa_aln_core] refine gapped alignments... 0.34 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 145227776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 145489920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.48 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 145752064 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.82 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 146014208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.74 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 146276352 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.84 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 146538496 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.82 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 146800640 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.84 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 147062784 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.80 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 147324928 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.77 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 147587072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.73 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 147849216 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.51 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 148111360 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.86 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 148373504 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.83 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 148635648 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.09 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 148897792 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.12 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 149159936 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 149422080 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 149684224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.94 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 149946368 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.67 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 150208512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.88 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 150470656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.88 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 150732800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.44 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 150994944 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 151257088 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.40 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 151519232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 151781376 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.06 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 152043520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.31 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 152305664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.90 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 152567808 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.62 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 152829952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.49 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 153092096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.62 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 153354240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.49 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 153616384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.16 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 153878528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 154140672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.75 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 154402816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 154664960 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.73 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 154927104 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 155189248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 155451392 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 155713536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 155975680 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.95 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 156237824 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.97 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 156499968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 156762112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.44 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 157024256 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.78 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 157286400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.11 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 157548544 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 157810688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.52 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 158072832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.58 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 158334976 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 158597120 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.73 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 158859264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.96 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 159121408 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 159383552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.58 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 159645696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.25 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 159907840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.16 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 160169984 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.00 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 160432128 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.58 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 160694272 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.55 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 160956416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.82 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 161218560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.36 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 161480704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 161742848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.04 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 162004992 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.77 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 162267136 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 162529280 sequences have been processed.
[bwa_read_seq] 3.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 162791424 sequences have been processed.
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.51 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 163053568 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.32 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 163315712 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.18 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 163577856 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 163840000 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 164102144 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.43 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 164364288 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.17 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 164626432 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.01 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 164888576 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.81 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 165150720 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.96 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 165412864 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.20 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 165675008 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 165937152 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... 0.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 166199296 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.76 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 166461440 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.69 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 166723584 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.16 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 166985728 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.79 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 167247872 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 167510016 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.72 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 167772160 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.19 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 168034304 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 168296448 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 168558592 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.54 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 168820736 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 169082880 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.69 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 169345024 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.65 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 169607168 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.39 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 169869312 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.21 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 170131456 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.82 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 170393600 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.92 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 170655744 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.67 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 170917888 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.55 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 171180032 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.82 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 171442176 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.74 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 171704320 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.47 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 171966464 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.92 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 172228608 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.73 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 172490752 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.14 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 172752896 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.90 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 173015040 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.68 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 173277184 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.96 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 173539328 sequences have been processed.
[bwa_read_seq] 10.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.79 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 173801472 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 174063616 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.95 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 174325760 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 174587904 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.30 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 174850048 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.88 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 175112192 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 175374336 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.60 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 175636480 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.28 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 175898624 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.56 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 176160768 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.34 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 176422912 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.00 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 176685056 sequences have been processed.
[bwa_read_seq] 3.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.36 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 176947200 sequences have been processed.
[bwa_read_seq] 2.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 177209344 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 177471488 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.63 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 177733632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 177995776 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.76 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 178257920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 178520064 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 178782208 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 179044352 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.75 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 179306496 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.61 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 179568640 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.28 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 179830784 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.81 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 180092928 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.65 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 180355072 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.73 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 180617216 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.54 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 180879360 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 181141504 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.83 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 181403648 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.09 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 181665792 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 181927936 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.71 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 182190080 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.48 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 182452224 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.83 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 182714368 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... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 182976512 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.21 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 183238656 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 183500800 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 183762944 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 184025088 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.26 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 184287232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 184549376 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 184811520 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.74 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 185073664 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.38 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 185335808 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.35 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 185597952 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.09 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 185860096 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 186122240 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 186384384 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.98 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 186646528 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.91 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 186908672 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 187170816 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 187432960 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 187695104 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.80 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 187957248 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.07 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 188219392 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.37 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 188481536 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.75 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 188743680 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.40 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 189005824 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.17 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 189267968 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 189530112 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.00 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 189792256 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.69 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 190054400 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.68 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 190316544 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.98 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 190578688 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.51 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 190840832 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 191102976 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.05 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 191365120 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.30 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 191627264 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.46 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 191889408 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 192151552 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 192413696 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.86 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 192675840 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 192937984 sequences have been processed.
[bwa_read_seq] 2.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 193200128 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.20 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 193462272 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 193724416 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.11 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 193986560 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.20 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 194248704 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.13 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 194510848 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.52 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 194772992 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.12 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 195035136 sequences have been processed.
[bwa_read_seq] 2.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.84 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 195297280 sequences have been processed.
[bwa_read_seq] 2.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.64 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 195559424 sequences have been processed.
[bwa_read_seq] 2.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.48 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 195821568 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.83 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 196083712 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 196345856 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.88 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 196608000 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.91 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 196870144 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.76 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 197132288 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 197394432 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.52 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 197656576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.30 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 197918720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.49 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 198180864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.90 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 198443008 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.46 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 198705152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 198967296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 199229440 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 199491584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 199753728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 200015872 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 200278016 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 200540160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 200802304 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 201064448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 201326592 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 201588736 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 201850880 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 202113024 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... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 202375168 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 202637312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 202899456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 203161600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 203423744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 203685888 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 203948032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 204210176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 204472320 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 204734464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 204996608 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 205258752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 205520896 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 205783040 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 206045184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.66 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 206307328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 206569472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 206831616 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 207093760 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 207355904 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 207618048 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 207880192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 208142336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 208404480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 208666624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 208928768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 209190912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.84 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 209453056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 209715200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 209977344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 210239488 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 210501632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 210763776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 211025920 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 211288064 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 211550208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 211812352 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 212074496 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 212336640 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 212598784 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 212860928 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 213123072 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 213385216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 213647360 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 213909504 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 214171648 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 214433792 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 214695936 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 214958080 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 215220224 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 215482368 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 215744512 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 216006656 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.64 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 216268800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 216530944 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 216793088 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 217055232 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 217317376 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 217579520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.59 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 217841664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.57 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 218103808 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 218365952 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 218628096 sequences have been processed.
[bwa_read_seq] 1.7% 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... 0.39 sec
[bwa_aln_core] 218890240 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 219152384 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 219414528 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.53 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 219676672 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.35 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 219938816 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 220200960 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 220463104 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 220725248 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 220987392 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 221249536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 221511680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 221773824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.32 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 222035968 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 222298112 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 222560256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 222822400 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 223084544 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 223346688 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 223608832 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.42 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 223870976 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.39 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 224133120 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 224395264 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 224657408 sequences have been processed.
[bwa_read_seq] 1.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.44 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 224919552 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 225181696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 225443840 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 225705984 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.34 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 225968128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 226230272 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 226492416 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 226754560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 227016704 sequences have been processed.
[bwa_read_seq] 1.2% 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... 0.46 sec
[bwa_aln_core] 227278848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 227540992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.36 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 227803136 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 228065280 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.91 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 228327424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 228589568 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 228851712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 229113856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 229376000 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 229638144 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... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 229900288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 230162432 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 230424576 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 230686720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 230948864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 231211008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 231473152 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 231735296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 231997440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 232259584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 232521728 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 232783872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.02 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 233046016 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 233308160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.11 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 233570304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 233832448 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 234094592 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 234356736 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 234618880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 234881024 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.33 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 235143168 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 235405312 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 235667456 sequences have been processed.
[bwa_read_seq] 1.1% 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... 0.40 sec
[bwa_aln_core] 235929600 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 236191744 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.20 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 236453888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.43 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 236716032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 236978176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 237240320 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 237502464 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 237764608 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... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 238026752 sequences have been processed.
[bwa_read_seq] 1.3% 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] 238288896 sequences have been processed.
[bwa_read_seq] 1.3% 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] 238551040 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 238813184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.73 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 239075328 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 239337472 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.61 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 239599616 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.53 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 239861760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 240123904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.62 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 240386048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.51 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 240648192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.76 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 240910336 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 241172480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 241434624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.38 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 241696768 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 241958912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.42 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 242221056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.10 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 242483200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.11 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 242745344 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.29 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 243007488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.01 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 243269632 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 243531776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 243793920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.68 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 244056064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.14 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 244318208 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.86 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 244580352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.42 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 244842496 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... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 245104640 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.82 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 245366784 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... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 245628928 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.44 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 245891072 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 246153216 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 246415360 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 246677504 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.31 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 246939648 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 247201792 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.08 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 247463936 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.18 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 247726080 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 247988224 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.15 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 248250368 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 248512512 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.58 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 248774656 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.23 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 249036800 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 249298944 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 249561088 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 249823232 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.43 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 250085376 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.78 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 250347520 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.88 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 250609664 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.11 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 250871808 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.84 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 251133952 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... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 251396096 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.52 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 251658240 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.00 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 251920384 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... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 252182528 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.04 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 252444672 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.84 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 252706816 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.67 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 252968960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.00 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 253231104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.97 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 253493248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.21 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 253755392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.81 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 254017536 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.30 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 254279680 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 254541824 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 254803968 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.57 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 255066112 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.48 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 255328256 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.66 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 255590400 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.41 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 255852544 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 256114688 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.82 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 256376832 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.33 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 256638976 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.99 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 256901120 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.72 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 257163264 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.39 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 257425408 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.40 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 257687552 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.60 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 257949696 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.36 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 258211840 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.73 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 258473984 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.74 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 258736128 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.81 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 258998272 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.46 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 259260416 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.22 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 259522560 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.07 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 259784704 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 260046848 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.08 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 260308992 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.16 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 260571136 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... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 260833280 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.13 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 261095424 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.66 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 261357568 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 261619712 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.97 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 261881856 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.76 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 262144000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.19 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 262406144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.70 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 262668288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.12 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 262930432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.66 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 263192576 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.69 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 263454720 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 263716864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.80 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 263979008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.67 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 264241152 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.48 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 264503296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 264765440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.49 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 265027584 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.84 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 265289728 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.82 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 265551872 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.56 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 265814016 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.64 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 266076160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.62 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 266338304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.95 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 266600448 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.94 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 266862592 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.36 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 267124736 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.63 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 267386880 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 267649024 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.90 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 267911168 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.33 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 268173312 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.40 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 268435456 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.44 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 268697600 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.04 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 268959744 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.09 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 269221888 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... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 269484032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.61 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 269746176 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.00 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 270008320 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.85 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 270270464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.42 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 270532608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.59 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 270794752 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.51 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 271056896 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 271319040 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.50 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 271581184 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.07 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 271843328 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... 0.42 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 272105472 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.58 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 272367616 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.33 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 272629760 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.60 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 272891904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 273154048 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 273416192 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.84 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 273678336 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.88 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 273940480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.17 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 274202624 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.87 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 274464768 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.09 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 274726912 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.69 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 274989056 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.03 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 275251200 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.91 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 275513344 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.59 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 275775488 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.58 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 276037632 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.41 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 276299776 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.03 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 276561920 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.65 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 276824064 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 277086208 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.12 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 277348352 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.72 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 277610496 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.85 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 277872640 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.60 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 278134784 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.42 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 278396928 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.62 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 278659072 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.47 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 278921216 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.99 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 279183360 sequences have been processed.
[bwa_read_seq] 16.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.03 sec
[bwa_aln_core] refine gapped alignments... 0.24 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 279183439 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/ZF4/out/align/rep1/ZF4_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF4_allReps.fastq.gz
[main] Real time: 14017.674 sec; CPU: 13494.588 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/ZF4/out/align/rep1/ZF4_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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/ZF4/out/align/rep1/ZF4_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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--------------------
22607 (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/ZF4/out/align/rep1/ZF4_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_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--------------------
29207 (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 08:55:16 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_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 08:55:16 PDT 2016] Executing as imk1@nandi on Linux 3.16.0-67-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-29 08:55:16	MarkDuplicates	Start of doWork freeMemory: 255389968; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-29 08:55:16	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-29 08:55:16	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-29 08:55:18	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836474.7991095'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2016-09-29 08:55:29	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:   11s.  Last read position: chr1:24,483,263
INFO	2016-09-29 08:55:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:55:37	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    7s.  Last read position: chr1:43,036,846
INFO	2016-09-29 08:55:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:55:51	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:33s.  Time for last 1,000,000:   14s.  Last read position: chr1:60,172,888
INFO	2016-09-29 08:55:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:55:54	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    2s.  Last read position: chr1:78,454,002
INFO	2016-09-29 08:55:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:07	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:   13s.  Last read position: chr1:94,821,130
INFO	2016-09-29 08:56:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:10	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    2s.  Last read position: chr1:115,545,379
INFO	2016-09-29 08:56:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:15	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    4s.  Last read position: chr1:133,509,726
INFO	2016-09-29 08:56:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:23	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    7s.  Last read position: chr1:148,931,058
INFO	2016-09-29 08:56:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:27	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    4s.  Last read position: chr1:162,625,082
INFO	2016-09-29 08:56:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:31	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    3s.  Last read position: chr1:177,255,067
INFO	2016-09-29 08:56:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:32	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:14s.  Time for last 1,000,000:    1s.  Last read position: chr1:191,980,870
INFO	2016-09-29 08:56:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:35	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    2s.  Last read position: chr2:17,021,868
INFO	2016-09-29 08:56:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:42	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:24s.  Time for last 1,000,000:    7s.  Last read position: chr2:31,090,031
INFO	2016-09-29 08:56:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:44	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    1s.  Last read position: chr2:45,108,562
INFO	2016-09-29 08:56:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:56:49	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:    5s.  Last read position: chr2:61,670,345
INFO	2016-09-29 08:56:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:02	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:   12s.  Last read position: chr2:76,372,642
INFO	2016-09-29 08:57:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:05	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    3s.  Last read position: chr2:93,175,579
INFO	2016-09-29 08:57:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:07	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    1s.  Last read position: chr2:108,625,174
INFO	2016-09-29 08:57:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:09	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    2s.  Last read position: chr2:123,758,487
INFO	2016-09-29 08:57:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:11	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    1s.  Last read position: chr2:138,279,311
INFO	2016-09-29 08:57:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:14	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:    2s.  Last read position: chr2:154,946,823
INFO	2016-09-29 08:57:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:16	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:01:57s.  Time for last 1,000,000:    1s.  Last read position: chr2:167,861,488
INFO	2016-09-29 08:57:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:18	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:    2s.  Last read position: chr3:9,234,742
INFO	2016-09-29 08:57:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:23	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    4s.  Last read position: chr3:30,975,643
INFO	2016-09-29 08:57:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:32	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    8s.  Last read position: chr3:51,584,079
INFO	2016-09-29 08:57:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:37	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:19s.  Time for last 1,000,000:    5s.  Last read position: chr3:68,869,899
INFO	2016-09-29 08:57:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:41	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    3s.  Last read position: chr3:86,488,943
INFO	2016-09-29 08:57:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:48	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:29s.  Time for last 1,000,000:    6s.  Last read position: chr3:98,407,936
INFO	2016-09-29 08:57:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:49	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:31s.  Time for last 1,000,000:    1s.  Last read position: chr3:113,629,543
INFO	2016-09-29 08:57:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:57:54	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chr3:129,970,001
INFO	2016-09-29 08:57:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:03	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:02:44s.  Time for last 1,000,000:    8s.  Last read position: chr3:144,683,511
INFO	2016-09-29 08:58:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:05	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:02:46s.  Time for last 1,000,000:    2s.  Last read position: chr4:6,239,923
INFO	2016-09-29 08:58:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:10	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:02:52s.  Time for last 1,000,000:    5s.  Last read position: chr4:26,437,461
INFO	2016-09-29 08:58:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:14	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:02:56s.  Time for last 1,000,000:    4s.  Last read position: chr4:44,717,681
INFO	2016-09-29 08:58:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:18	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:03:00s.  Time for last 1,000,000:    4s.  Last read position: chr4:62,379,630
INFO	2016-09-29 08:58:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:20	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:03:02s.  Time for last 1,000,000:    1s.  Last read position: chr4:83,968,737
INFO	2016-09-29 08:58:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:22	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:03:04s.  Time for last 1,000,000:    1s.  Last read position: chr4:102,562,119
INFO	2016-09-29 08:58:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:24	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:03:06s.  Time for last 1,000,000:    1s.  Last read position: chr4:118,920,262
INFO	2016-09-29 08:58:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:28	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:03:09s.  Time for last 1,000,000:    3s.  Last read position: chr4:132,768,606
INFO	2016-09-29 08:58:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:29	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:03:11s.  Time for last 1,000,000:    1s.  Last read position: chr4:144,473,842
INFO	2016-09-29 08:58:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:32	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:03:14s.  Time for last 1,000,000:    2s.  Last read position: chr5:8,055,940
INFO	2016-09-29 08:58:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:35	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:03:17s.  Time for last 1,000,000:    2s.  Last read position: chr5:28,791,427
INFO	2016-09-29 08:58:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:39	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:03:21s.  Time for last 1,000,000:    4s.  Last read position: chr5:44,736,043
INFO	2016-09-29 08:58:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:49	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:   10s.  Last read position: chr5:64,765,297
INFO	2016-09-29 08:58:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:58:54	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:03:36s.  Time for last 1,000,000:    4s.  Last read position: chr5:81,784,793
INFO	2016-09-29 08:58:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:03	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:03:44s.  Time for last 1,000,000:    8s.  Last read position: chr5:101,785,183
INFO	2016-09-29 08:59:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:06	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:03:48s.  Time for last 1,000,000:    3s.  Last read position: chr5:116,845,804
INFO	2016-09-29 08:59:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:11	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:03:53s.  Time for last 1,000,000:    5s.  Last read position: chr5:130,846,057
INFO	2016-09-29 08:59:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:15	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:03:56s.  Time for last 1,000,000:    3s.  Last read position: chr5:145,281,863
INFO	2016-09-29 08:59:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:18	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:    3s.  Last read position: chr6:14,168,565
INFO	2016-09-29 08:59:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:20	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:04:02s.  Time for last 1,000,000:    2s.  Last read position: chr6:32,073,856
INFO	2016-09-29 08:59:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:23	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:04:04s.  Time for last 1,000,000:    2s.  Last read position: chr6:49,218,736
INFO	2016-09-29 08:59:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:25	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    1s.  Last read position: chr6:67,191,574
INFO	2016-09-29 08:59:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:26	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:04:08s.  Time for last 1,000,000:    1s.  Last read position: chr6:86,305,244
INFO	2016-09-29 08:59:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:30	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:04:12s.  Time for last 1,000,000:    3s.  Last read position: chr6:101,959,598
INFO	2016-09-29 08:59:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:32	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:04:14s.  Time for last 1,000,000:    2s.  Last read position: chr6:119,320,626
INFO	2016-09-29 08:59:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:37	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:04:19s.  Time for last 1,000,000:    4s.  Last read position: chr6:134,792,200
INFO	2016-09-29 08:59:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:40	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:04:21s.  Time for last 1,000,000:    2s.  Last read position: chr7:4,548,840
INFO	2016-09-29 08:59:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:42	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:    2s.  Last read position: chr7:28,809,587
INFO	2016-09-29 08:59:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 08:59:52	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:04:34s.  Time for last 1,000,000:    9s.  Last read position: chr7:48,153,071
INFO	2016-09-29 08:59:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:00	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:04:42s.  Time for last 1,000,000:    8s.  Last read position: chr7:70,240,256
INFO	2016-09-29 09:00:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:03	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    2s.  Last read position: chr7:86,869,281
INFO	2016-09-29 09:00:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:07	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:04:49s.  Time for last 1,000,000:    4s.  Last read position: chr7:101,649,635
INFO	2016-09-29 09:00:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:13	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:04:54s.  Time for last 1,000,000:    5s.  Last read position: chr7:117,734,381
INFO	2016-09-29 09:00:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:16	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    3s.  Last read position: chr7:131,556,799
INFO	2016-09-29 09:00:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:19	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:    2s.  Last read position: chr8:6,948,976
INFO	2016-09-29 09:00:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:24	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:05:05s.  Time for last 1,000,000:    4s.  Last read position: chr8:28,420,250
INFO	2016-09-29 09:00:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:26	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:05:07s.  Time for last 1,000,000:    2s.  Last read position: chr8:47,948,924
INFO	2016-09-29 09:00:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:28	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:05:10s.  Time for last 1,000,000:    2s.  Last read position: chr8:68,881,811
INFO	2016-09-29 09:00:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:30	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    2s.  Last read position: chr8:84,065,161
INFO	2016-09-29 09:00:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:32	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    2s.  Last read position: chr8:101,115,207
INFO	2016-09-29 09:00:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:36	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:05:18s.  Time for last 1,000,000:    3s.  Last read position: chr8:117,226,469
INFO	2016-09-29 09:00:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:38	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:05:20s.  Time for last 1,000,000:    1s.  Last read position: chr9:4,983,700
INFO	2016-09-29 09:00:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:41	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:05:22s.  Time for last 1,000,000:    2s.  Last read position: chr9:23,901,613
INFO	2016-09-29 09:00:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:44	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:05:26s.  Time for last 1,000,000:    3s.  Last read position: chr9:43,398,066
INFO	2016-09-29 09:00:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:55	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:05:37s.  Time for last 1,000,000:   11s.  Last read position: chr9:58,004,158
INFO	2016-09-29 09:00:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:00:57	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:05:39s.  Time for last 1,000,000:    1s.  Last read position: chr9:70,866,341
INFO	2016-09-29 09:00:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:00	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:    2s.  Last read position: chr9:86,464,895
INFO	2016-09-29 09:01:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:07	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:05:49s.  Time for last 1,000,000:    7s.  Last read position: chr9:104,181,972
INFO	2016-09-29 09:01:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:09	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:05:51s.  Time for last 1,000,000:    2s.  Last read position: chr9:119,116,002
INFO	2016-09-29 09:01:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:11	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:05:53s.  Time for last 1,000,000:    1s.  Last read position: chr10:14,470,649
INFO	2016-09-29 09:01:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:13	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    1s.  Last read position: chr10:31,131,955
INFO	2016-09-29 09:01:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:15	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:05:56s.  Time for last 1,000,000:    1s.  Last read position: chr10:47,989,134
INFO	2016-09-29 09:01:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:16	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:05:58s.  Time for last 1,000,000:    1s.  Last read position: chr10:64,630,041
INFO	2016-09-29 09:01:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:18	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:06:00s.  Time for last 1,000,000:    1s.  Last read position: chr10:80,016,583
INFO	2016-09-29 09:01:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:22	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:06:04s.  Time for last 1,000,000:    3s.  Last read position: chr10:93,497,127
INFO	2016-09-29 09:01:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:24	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:06:06s.  Time for last 1,000,000:    2s.  Last read position: chr10:108,859,337
INFO	2016-09-29 09:01:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:29	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:06:11s.  Time for last 1,000,000:    4s.  Last read position: chr10:124,533,500
INFO	2016-09-29 09:01:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:34	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:06:16s.  Time for last 1,000,000:    5s.  Last read position: chr11:11,686,608
INFO	2016-09-29 09:01:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:39	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:06:21s.  Time for last 1,000,000:    5s.  Last read position: chr11:28,996,811
INFO	2016-09-29 09:01:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:51	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:06:32s.  Time for last 1,000,000:   11s.  Last read position: chr11:46,348,963
INFO	2016-09-29 09:01:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:53	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:06:35s.  Time for last 1,000,000:    2s.  Last read position: chr11:60,701,181
INFO	2016-09-29 09:01:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:01:58	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:06:40s.  Time for last 1,000,000:    5s.  Last read position: chr11:74,539,747
INFO	2016-09-29 09:01:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:03	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:06:45s.  Time for last 1,000,000:    5s.  Last read position: chr11:85,627,052
INFO	2016-09-29 09:02:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:05	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:    1s.  Last read position: chr11:98,201,788
INFO	2016-09-29 09:02:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:07	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:06:49s.  Time for last 1,000,000:    1s.  Last read position: chr11:108,531,221
INFO	2016-09-29 09:02:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:09	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:06:51s.  Time for last 1,000,000:    1s.  Last read position: chr11:120,598,765
INFO	2016-09-29 09:02:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:11	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:06:53s.  Time for last 1,000,000:    1s.  Last read position: chr12:25,629,036
INFO	2016-09-29 09:02:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:13	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    1s.  Last read position: chr12:44,340,582
INFO	2016-09-29 09:02:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:15	MarkDuplicates	Read   100,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:    1s.  Last read position: chr12:65,075,221
INFO	2016-09-29 09:02:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:19	MarkDuplicates	Read   101,000,000 records.  Elapsed time: 00:07:00s.  Time for last 1,000,000:    3s.  Last read position: chr12:80,222,063
INFO	2016-09-29 09:02:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:21	MarkDuplicates	Read   102,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    2s.  Last read position: chr12:97,145,833
INFO	2016-09-29 09:02:21	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:27	MarkDuplicates	Read   103,000,000 records.  Elapsed time: 00:07:09s.  Time for last 1,000,000:    5s.  Last read position: chr12:112,631,909
INFO	2016-09-29 09:02:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:31	MarkDuplicates	Read   104,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    4s.  Last read position: chr13:14,980,527
INFO	2016-09-29 09:02:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:35	MarkDuplicates	Read   105,000,000 records.  Elapsed time: 00:07:16s.  Time for last 1,000,000:    3s.  Last read position: chr13:32,028,863
INFO	2016-09-29 09:02:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:37	MarkDuplicates	Read   106,000,000 records.  Elapsed time: 00:07:19s.  Time for last 1,000,000:    2s.  Last read position: chr13:46,900,419
INFO	2016-09-29 09:02:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:45	MarkDuplicates	Read   107,000,000 records.  Elapsed time: 00:07:27s.  Time for last 1,000,000:    8s.  Last read position: chr13:64,057,947
INFO	2016-09-29 09:02:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:47	MarkDuplicates	Read   108,000,000 records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:    2s.  Last read position: chr13:84,347,054
INFO	2016-09-29 09:02:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:51	MarkDuplicates	Read   109,000,000 records.  Elapsed time: 00:07:32s.  Time for last 1,000,000:    3s.  Last read position: chr13:100,834,153
INFO	2016-09-29 09:02:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:53	MarkDuplicates	Read   110,000,000 records.  Elapsed time: 00:07:34s.  Time for last 1,000,000:    1s.  Last read position: chr13:116,010,761
INFO	2016-09-29 09:02:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:55	MarkDuplicates	Read   111,000,000 records.  Elapsed time: 00:07:36s.  Time for last 1,000,000:    2s.  Last read position: chr14:23,270,532
INFO	2016-09-29 09:02:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:57	MarkDuplicates	Read   112,000,000 records.  Elapsed time: 00:07:38s.  Time for last 1,000,000:    1s.  Last read position: chr14:45,165,044
INFO	2016-09-29 09:02:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:02:59	MarkDuplicates	Read   113,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:    2s.  Last read position: chr14:61,709,665
INFO	2016-09-29 09:02:59	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:01	MarkDuplicates	Read   114,000,000 records.  Elapsed time: 00:07:43s.  Time for last 1,000,000:    1s.  Last read position: chr14:76,910,837
INFO	2016-09-29 09:03:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:03	MarkDuplicates	Read   115,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:    2s.  Last read position: chr14:95,613,594
INFO	2016-09-29 09:03:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:08	MarkDuplicates	Read   116,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    4s.  Last read position: chr14:113,887,836
INFO	2016-09-29 09:03:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:10	MarkDuplicates	Read   117,000,000 records.  Elapsed time: 00:07:52s.  Time for last 1,000,000:    1s.  Last read position: chr15:10,245,188
INFO	2016-09-29 09:03:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:13	MarkDuplicates	Read   118,000,000 records.  Elapsed time: 00:07:55s.  Time for last 1,000,000:    2s.  Last read position: chr15:32,417,454
INFO	2016-09-29 09:03:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:16	MarkDuplicates	Read   119,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:    3s.  Last read position: chr15:52,667,897
INFO	2016-09-29 09:03:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:19	MarkDuplicates	Read   120,000,000 records.  Elapsed time: 00:08:01s.  Time for last 1,000,000:    3s.  Last read position: chr15:69,800,934
INFO	2016-09-29 09:03:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:23	MarkDuplicates	Read   121,000,000 records.  Elapsed time: 00:08:04s.  Time for last 1,000,000:    3s.  Last read position: chr15:82,429,071
INFO	2016-09-29 09:03:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:31	MarkDuplicates	Read   122,000,000 records.  Elapsed time: 00:08:13s.  Time for last 1,000,000:    8s.  Last read position: chr15:98,778,984
INFO	2016-09-29 09:03:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:33	MarkDuplicates	Read   123,000,000 records.  Elapsed time: 00:08:14s.  Time for last 1,000,000:    1s.  Last read position: chr16:12,002,392
INFO	2016-09-29 09:03:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:36	MarkDuplicates	Read   124,000,000 records.  Elapsed time: 00:08:18s.  Time for last 1,000,000:    3s.  Last read position: chr16:27,918,267
INFO	2016-09-29 09:03:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:42	MarkDuplicates	Read   125,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:    5s.  Last read position: chr16:43,100,622
INFO	2016-09-29 09:03:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:44	MarkDuplicates	Read   126,000,000 records.  Elapsed time: 00:08:25s.  Time for last 1,000,000:    1s.  Last read position: chr16:58,547,995
INFO	2016-09-29 09:03:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:45	MarkDuplicates	Read   127,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:    1s.  Last read position: chr16:77,095,432
INFO	2016-09-29 09:03:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:47	MarkDuplicates	Read   128,000,000 records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:    2s.  Last read position: chr16:94,000,151
INFO	2016-09-29 09:03:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:49	MarkDuplicates	Read   129,000,000 records.  Elapsed time: 00:08:31s.  Time for last 1,000,000:    1s.  Last read position: chr17:17,826,704
INFO	2016-09-29 09:03:49	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:51	MarkDuplicates	Read   130,000,000 records.  Elapsed time: 00:08:33s.  Time for last 1,000,000:    1s.  Last read position: chr17:31,445,773
INFO	2016-09-29 09:03:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:53	MarkDuplicates	Read   131,000,000 records.  Elapsed time: 00:08:35s.  Time for last 1,000,000:    1s.  Last read position: chr17:42,873,148
INFO	2016-09-29 09:03:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:55	MarkDuplicates	Read   132,000,000 records.  Elapsed time: 00:08:37s.  Time for last 1,000,000:    1s.  Last read position: chr17:57,770,801
INFO	2016-09-29 09:03:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:03:57	MarkDuplicates	Read   133,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:    1s.  Last read position: chr17:75,926,728
INFO	2016-09-29 09:03:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:02	MarkDuplicates	Read   134,000,000 records.  Elapsed time: 00:08:44s.  Time for last 1,000,000:    4s.  Last read position: chr17:90,882,674
INFO	2016-09-29 09:04:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:04	MarkDuplicates	Read   135,000,000 records.  Elapsed time: 00:08:45s.  Time for last 1,000,000:    1s.  Last read position: chr18:20,856,277
INFO	2016-09-29 09:04:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:08	MarkDuplicates	Read   136,000,000 records.  Elapsed time: 00:08:50s.  Time for last 1,000,000:    4s.  Last read position: chr18:37,755,487
INFO	2016-09-29 09:04:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:16	MarkDuplicates	Read   137,000,000 records.  Elapsed time: 00:08:58s.  Time for last 1,000,000:    8s.  Last read position: chr18:56,262,406
INFO	2016-09-29 09:04:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:19	MarkDuplicates	Read   138,000,000 records.  Elapsed time: 00:09:01s.  Time for last 1,000,000:    2s.  Last read position: chr18:71,962,002
INFO	2016-09-29 09:04:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:22	MarkDuplicates	Read   139,000,000 records.  Elapsed time: 00:09:04s.  Time for last 1,000,000:    3s.  Last read position: chr18:89,605,359
INFO	2016-09-29 09:04:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:25	MarkDuplicates	Read   140,000,000 records.  Elapsed time: 00:09:07s.  Time for last 1,000,000:    3s.  Last read position: chr19:16,328,482
INFO	2016-09-29 09:04:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:29	MarkDuplicates	Read   141,000,000 records.  Elapsed time: 00:09:10s.  Time for last 1,000,000:    3s.  Last read position: chr19:33,526,937
INFO	2016-09-29 09:04:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:32	MarkDuplicates	Read   142,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:    3s.  Last read position: chr19:46,828,230
INFO	2016-09-29 09:04:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:35	MarkDuplicates	Read   143,000,000 records.  Elapsed time: 00:09:17s.  Time for last 1,000,000:    3s.  Last read position: chrX:10,627,254
INFO	2016-09-29 09:04:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:40	MarkDuplicates	Read   144,000,000 records.  Elapsed time: 00:09:22s.  Time for last 1,000,000:    5s.  Last read position: chrX:61,731,388
INFO	2016-09-29 09:04:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:42	MarkDuplicates	Read   145,000,000 records.  Elapsed time: 00:09:24s.  Time for last 1,000,000:    1s.  Last read position: chrX:103,215,420
INFO	2016-09-29 09:04:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:44	MarkDuplicates	Read   146,000,000 records.  Elapsed time: 00:09:26s.  Time for last 1,000,000:    1s.  Last read position: chrX:142,976,233
INFO	2016-09-29 09:04:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:46	MarkDuplicates	Read   147,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    2s.  Last read position: GL456378.1:5,129
INFO	2016-09-29 09:04:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 09:04:46	MarkDuplicates	Read 147062688 records. 0 pairs never matched.
INFO	2016-09-29 09:04:52	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2393067240; totalMemory: 2480275456; maxMemory: 3817799680
INFO	2016-09-29 09:04:52	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-29 09:04:52	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-29 09:04:52	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-29 09:05:23	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-29 09:05:28	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2180065056; totalMemory: 3160866816; maxMemory: 3817799680
INFO	2016-09-29 09:05:28	MarkDuplicates	Marking 97913264 records as duplicates.
INFO	2016-09-29 09:05:28	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-29 09:06:53	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:24s.  Time for last 10,000,000:   84s.  Last read position: chr1:177,255,067
INFO	2016-09-29 09:08:17	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:49s.  Time for last 10,000,000:   84s.  Last read position: chr2:138,279,311
INFO	2016-09-29 09:09:43	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:14s.  Time for last 10,000,000:   85s.  Last read position: chr3:129,970,001
INFO	2016-09-29 09:11:07	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:38s.  Time for last 10,000,000:   84s.  Last read position: chr4:144,473,842
INFO	2016-09-29 09:12:31	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:02s.  Time for last 10,000,000:   83s.  Last read position: chr6:14,168,565
INFO	2016-09-29 09:13:55	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:26s.  Time for last 10,000,000:   83s.  Last read position: chr7:48,153,071
INFO	2016-09-29 09:15:19	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:50s.  Time for last 10,000,000:   84s.  Last read position: chr8:84,065,161
INFO	2016-09-29 09:16:43	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:14s.  Time for last 10,000,000:   84s.  Last read position: chr9:119,116,002
INFO	2016-09-29 09:18:08	MarkDuplicates	Written    90,000,000 records.  Elapsed time: 00:12:40s.  Time for last 10,000,000:   85s.  Last read position: chr11:28,996,811
INFO	2016-09-29 09:19:33	MarkDuplicates	Written   100,000,000 records.  Elapsed time: 00:14:04s.  Time for last 10,000,000:   84s.  Last read position: chr12:65,075,221
INFO	2016-09-29 09:20:56	MarkDuplicates	Written   110,000,000 records.  Elapsed time: 00:15:27s.  Time for last 10,000,000:   83s.  Last read position: chr13:116,010,761
INFO	2016-09-29 09:22:21	MarkDuplicates	Written   120,000,000 records.  Elapsed time: 00:16:53s.  Time for last 10,000,000:   85s.  Last read position: chr15:69,800,934
INFO	2016-09-29 09:23:47	MarkDuplicates	Written   130,000,000 records.  Elapsed time: 00:18:18s.  Time for last 10,000,000:   85s.  Last read position: chr17:31,445,773
INFO	2016-09-29 09:25:13	MarkDuplicates	Written   140,000,000 records.  Elapsed time: 00:19:44s.  Time for last 10,000,000:   85s.  Last read position: chr19:16,328,482
INFO	2016-09-29 09:26:13	MarkDuplicates	Before output close freeMemory: 3290931488; totalMemory: 3320774656; maxMemory: 3817799680
INFO	2016-09-29 09:26:13	MarkDuplicates	After output close freeMemory: 3290933280; totalMemory: 3320774656; maxMemory: 3817799680
[Thu Sep 29 09:26:14 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 30.96 minutes.
Runtime.totalMemory()=3320774656

 

 
# 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/ZF4/out/align/rep1/ZF4_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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/ZF4/out/qc/rep1/ZF4_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--------------------
17859 (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/ZF4/out/align/rep1/ZF4_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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--------------------
7312 (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/ZF4/out/align/rep1/ZF4_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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--------------------
19390 (process ID) old priority 0, new priority 10
Waiting for 25 seconds.

 
--------------------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/ZF4/out/align/rep1/ZF4_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/ZF4/out/align/rep1/ZF4_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_allReps.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_allReps.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_allReps.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr2/ZF4_allReps.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/pseudo_reps/rep1/pr1/ZF4_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--------------------
7390 (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/ZF4/out/align/rep1/ZF4_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_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--------------------
22845 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_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/ZF4/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/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/qc/rep1/ZF4_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9807.1.q/Rtmpg3bd0h/ZF4_allReps.nodup.15M.tagAlign597f58757d40
done. read 15000000 fragments
ChIP data read length 50 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1949454 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.209522552035129,0.209372957137669,0.203333967757757 
Top 3 estimates for fragment length 100,115,265 
Window half size 540 
Phantom peak location 55 
Phantom peak Correlation 0.2068564 
Normalized Strand cross-correlation coefficient (NSC) 1.074776 
Relative Strand Cross correlation Coefficient (RSC) 1.223843 
Phantom Peak Quality Tag 1 
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/ZF4/out/align/rep1/ZF4_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1 -speak=100 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_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/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_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--------------------
19923 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/rep1/ZF4_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 100 
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/ZF4/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/peak/spp/rep1/ZF4_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/ZF4/out/align/rep1/ZF4_allReps.nodup.tagAlign.gz 
opened /tmp/9808.1.q/Rtmp9V7UJp/ZF4_allReps.nodup.tagAlign4e1a4e5363c4
done. read 49149424 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF4/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9808.1.q/Rtmp9V7UJp/mousePrimaryBCellInput.nodup.tagAlign4e1a3f6a1c
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.427856 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.459532396234227 
Top 3 estimates for fragment length 100 
Window half size 550 
Phantom peak location 55 
Phantom peak Correlation 0.4537827 
Normalized Strand cross-correlation coefficient (NSC) 1.074035 
Relative Strand Cross correlation Coefficient (RSC) 1.221767 
Phantom Peak Quality Tag 1 
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= 0.3431716  
 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools