chipseq.bds.20160928_164853_947/task.callpeak_spp.spp_rep1.line_54.id_25
chipseq.bds.20160928_164853_947/task.callpeak_idr.idr_final_qc.line_205.id_26
chipseq.bds.20160928_164853_947/task.graphviz.report.line_97.id_27
chipseq.bds.20160928_164853_947/task.report.pdf2png.line_324.id_32
 

 chipseq.bds.20160928_164853_947_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10
chipseq.bds.20160928_164853_947_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12
chipseq.bds.20160928_164853_947_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13
chipseq.bds.20160928_164853_947_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14
chipseq.bds.20160928_164853_947_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15
chipseq.bds.20160928_164853_947_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16
 

 chipseq.bds.20160928_164853_947_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11
chipseq.bds.20160928_164853_947_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23
chipseq.bds.20160928_164853_947_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24
 

 
# SYS command. line 110

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

# SYS command. line 113

 bwa aln -q 5 -l 32 -k 2 -t 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/ZF11/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--------------------
5800 (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... 34.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.93 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... 29.83 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... 29.42 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.29 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... 29.50 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.38 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... 29.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.37 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.39 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... 30.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.46 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... 31.64 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.98 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.29 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... 32.12 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.16 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... 29.66 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... 31.14 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... 29.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.40 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.32 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 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... 29.37 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.26 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.45 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... 29.53 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.46 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... 33.61 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... 29.88 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... 29.33 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.51 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... 29.22 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... 29.30 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... 29.23 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.43 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... 29.34 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... 29.39 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... 29.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.44 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... 29.65 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... 29.58 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... 31.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.24 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.06 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.74 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... 33.47 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... 33.05 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 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... 30.10 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.89 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... 29.79 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... 29.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.92 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.04 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... 31.38 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.97 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.93 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... 30.42 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... 29.91 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.46 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... 29.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.95 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.54 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... 32.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.51 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.67 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.62 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.22 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.52 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 29.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 28.77 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 27.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 7.42 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: 2779.002 sec; CPU: 2780.488 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/ZF11_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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--------------------
12319 (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] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.56 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.75 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.95 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.80 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.33 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.94 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.36 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.96 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.67 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.73 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.63 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.95 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.40 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.56 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.22 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.28 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.88 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.78 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.79 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.10 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.04 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.90 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.83 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.35 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.78 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.21 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.92 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.89 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.56 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.43 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.48 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.07 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.02 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.24 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.55 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.32 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.62 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.69 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.19 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 53.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.63 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.04 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 224.27 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 218.63 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 217.56 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.62 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 234.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 197.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 203.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 227.46 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 226.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 222.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.27 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 198.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 215.96 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 209.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 208.45 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 218.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 221.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 240.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 223.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 209.11 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 204.42 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 194.08 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 193.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 196.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 186.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 191.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 158.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 160.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 215.01 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 200.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 211.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 189.68 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.51 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 177.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 184.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 181.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.80 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 153.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 159.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 152.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 157.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.25 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 163.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 210.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 203.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 195.32 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 170.24 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.98 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.44 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.22 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 162.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 179.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 171.26 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 183.26 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 165.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 176.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 182.74 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 154.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 201.05 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 232.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 221.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.93 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 185.98 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.43 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 187.94 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.58 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 214.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 178.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 172.65 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.54 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 199.54 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 207.63 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 226.71 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 216.80 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 215.37 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 202.38 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 190.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 220.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 216.08 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 205.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 208.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 175.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 188.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 209.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 241.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 74.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.13 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.18 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.00 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.81 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.03 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.18 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.91 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.66 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.57 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.28 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.61 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.89 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.69 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.54 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.65 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.02 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.89 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.45 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.94 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.99 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.36 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.00 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.61 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.55 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.36 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.30 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.77 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.82 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.85 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.61 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.86 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.98 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.12 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.15 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.29 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.48 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.50 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.16 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.60 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.91 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.52 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.99 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.79 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.17 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.84 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 46.44 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.69 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.33 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 45.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.57 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.10 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 42.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 40.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 6.91 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 87862603 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/ZF11_allReps.fastq.gz
[main] Real time: 9741.538 sec; CPU: 30493.538 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/ZF11/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/ZF11/out/align/ctl1/mousePrimaryBCellInput.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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--------------------
4164 (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... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.44 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.49 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.45 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.41 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.68 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.65 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.50 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.58 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.05 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.77 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.21 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.89 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.98 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.09 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.44 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.12 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.28 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.56 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 7864320 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... 0.51 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% 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... 0.36 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.18 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.29 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.74 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.37 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.63 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.04 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.19 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.79 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.40 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... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.03 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% 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... 0.43 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.72 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.71 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 1.92 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.18 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/ZF11/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz
[main] Real time: 488.094 sec; CPU: 409.124 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/ZF11/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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/ZF11/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.bam | \
			    	sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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--------------------
11998 (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/ZF11/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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/ZF11/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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--------------------
5221 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Sep 28 17:58:21 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/ctl1/mousePrimaryBCellInput.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Sep 28 17:58:21 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-28 17:58:21	MarkDuplicates	Start of doWork freeMemory: 255390112; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-28 17:58:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-28 17:58:21	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
INFO	2016-09-28 17:58:24	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:174,151,470
INFO	2016-09-28 17:58:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:27	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr2:135,780,411
INFO	2016-09-28 17:58:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:30	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr3:122,530,375
INFO	2016-09-28 17:58:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:39	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    9s.  Last read position: chr4:135,044,888
INFO	2016-09-28 17:58:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:42	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    2s.  Last read position: chr5:135,067,778
INFO	2016-09-28 17:58:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:47	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:    5s.  Last read position: chr6:144,681,933
INFO	2016-09-28 17:58:47	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:53	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:31s.  Time for last 1,000,000:    5s.  Last read position: chr8:12,749,386
INFO	2016-09-28 17:58:53	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:58:58	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    5s.  Last read position: chr9:42,425,131
INFO	2016-09-28 17:58:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:02	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:41s.  Time for last 1,000,000:    3s.  Last read position: chr10:69,658,983
INFO	2016-09-28 17:59:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:09	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:    7s.  Last read position: chr11:86,536,377
INFO	2016-09-28 17:59:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:14	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    4s.  Last read position: chr13:6,026,344
INFO	2016-09-28 17:59:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:17	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:56s.  Time for last 1,000,000:    3s.  Last read position: chr14:54,434,282
INFO	2016-09-28 17:59:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:25	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:03s.  Time for last 1,000,000:    7s.  Last read position: chr15:98,839,731
INFO	2016-09-28 17:59:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:27	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chr17:62,456,013
INFO	2016-09-28 17:59:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:30	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:09s.  Time for last 1,000,000:    3s.  Last read position: chr19:38,585,732
INFO	2016-09-28 17:59:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-28 17:59:39	MarkDuplicates	Read 15489502 records. 0 pairs never matched.
INFO	2016-09-28 17:59:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2502111328; totalMemory: 2588409856; maxMemory: 3817799680
INFO	2016-09-28 17:59:40	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-28 17:59:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-28 17:59:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-28 17:59:44	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-28 17:59:45	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1987932048; totalMemory: 2963668992; maxMemory: 3817799680
INFO	2016-09-28 17:59:45	MarkDuplicates	Marking 157890 records as duplicates.
INFO	2016-09-28 17:59:45	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-28 18:01:32	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:47s.  Time for last 10,000,000:  107s.  Last read position: chr11:86,536,377
INFO	2016-09-28 18:02:38	MarkDuplicates	Before output close freeMemory: 2921519744; totalMemory: 2949185536; maxMemory: 3817799680
INFO	2016-09-28 18:02:39	MarkDuplicates	After output close freeMemory: 2950944568; totalMemory: 2978611200; maxMemory: 3817799680
[Wed Sep 28 18:02:39 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 4.31 minutes.
Runtime.totalMemory()=2978611200

 

 
# 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/ZF11/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 153

 sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/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/ZF11/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--------------------
13371 (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/ZF11/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/ZF11/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--------------------
5516 (process ID) old priority 0, new priority 10

Waiting for 27 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/ZF11/out/align/rep1/ZF11_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF11_allReps.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.bam

# SYS command. line 149

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_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--------------------
21127 (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] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.47 sec
[bwa_aln_core] refine gapped alignments... 9.07 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.56 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.42 sec
[bwa_aln_core] refine gapped alignments... 8.97 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.93 sec
[bwa_aln_core] refine gapped alignments... 9.08 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.13 sec
[bwa_aln_core] refine gapped alignments... 9.06 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.47 sec
[bwa_aln_core] refine gapped alignments... 5.92 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.16 sec
[bwa_aln_core] refine gapped alignments... 6.24 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.28 sec
[bwa_aln_core] refine gapped alignments... 6.12 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.12 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.40 sec
[bwa_aln_core] refine gapped alignments... 6.13 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.23 sec
[bwa_aln_core] refine gapped alignments... 6.12 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.91 sec
[bwa_aln_core] refine gapped alignments... 6.16 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.39 sec
[bwa_aln_core] refine gapped alignments... 6.11 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.31 sec
[bwa_aln_core] refine gapped alignments... 5.89 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.60 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.73 sec
[bwa_aln_core] refine gapped alignments... 9.78 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.94 sec
[bwa_aln_core] refine gapped alignments... 2.74 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.97 sec
[bwa_aln_core] refine gapped alignments... 6.11 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.54 sec
[bwa_aln_core] refine gapped alignments... 5.88 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.04 sec
[bwa_aln_core] refine gapped alignments... 6.16 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.37 sec
[bwa_aln_core] refine gapped alignments... 6.13 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.00 sec
[bwa_aln_core] refine gapped alignments... 6.03 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.77 sec
[bwa_aln_core] refine gapped alignments... 5.96 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.61 sec
[bwa_aln_core] refine gapped alignments... 5.74 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.59 sec
[bwa_aln_core] refine gapped alignments... 6.06 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.23 sec
[bwa_aln_core] refine gapped alignments... 6.03 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.50 sec
[bwa_aln_core] refine gapped alignments... 6.00 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.48 sec
[bwa_aln_core] refine gapped alignments... 3.51 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 81.93 sec
[bwa_aln_core] refine gapped alignments... 10.84 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.31 sec
[bwa_aln_core] refine gapped alignments... 9.25 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.07 sec
[bwa_aln_core] refine gapped alignments... 9.07 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.02 sec
[bwa_aln_core] refine gapped alignments... 9.13 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.08 sec
[bwa_aln_core] refine gapped alignments... 5.86 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.05 sec
[bwa_aln_core] refine gapped alignments... 9.26 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 61.32 sec
[bwa_aln_core] refine gapped alignments... 8.79 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 99.68 sec
[bwa_aln_core] refine gapped alignments... 19.26 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 90.78 sec
[bwa_aln_core] refine gapped alignments... 13.09 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.68 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.04 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.93 sec
[bwa_aln_core] refine gapped alignments... 0.93 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.56 sec
[bwa_aln_core] refine gapped alignments... 4.08 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.90 sec
[bwa_aln_core] refine gapped alignments... 1.63 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.21 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.63 sec
[bwa_aln_core] refine gapped alignments... 2.56 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.75 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.36 sec
[bwa_aln_core] refine gapped alignments... 7.61 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.91 sec
[bwa_aln_core] refine gapped alignments... 7.61 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.79 sec
[bwa_aln_core] refine gapped alignments... 4.08 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.32 sec
[bwa_aln_core] refine gapped alignments... 8.21 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.70 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.26 sec
[bwa_aln_core] refine gapped alignments... 6.96 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.04 sec
[bwa_aln_core] refine gapped alignments... 7.35 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.95 sec
[bwa_aln_core] refine gapped alignments... 8.08 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.32 sec
[bwa_aln_core] refine gapped alignments... 7.39 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.15 sec
[bwa_aln_core] refine gapped alignments... 7.41 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.04 sec
[bwa_aln_core] refine gapped alignments... 7.39 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.77 sec
[bwa_aln_core] refine gapped alignments... 8.15 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.75 sec
[bwa_aln_core] refine gapped alignments... 8.31 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.71 sec
[bwa_aln_core] refine gapped alignments... 8.14 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.02 sec
[bwa_aln_core] refine gapped alignments... 6.69 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.54 sec
[bwa_aln_core] refine gapped alignments... 7.28 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.77 sec
[bwa_aln_core] refine gapped alignments... 7.19 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.90 sec
[bwa_aln_core] refine gapped alignments... 7.16 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.18 sec
[bwa_aln_core] refine gapped alignments... 7.12 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.11 sec
[bwa_aln_core] refine gapped alignments... 8.20 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.39 sec
[bwa_aln_core] refine gapped alignments... 7.04 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.44 sec
[bwa_aln_core] refine gapped alignments... 7.06 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.83 sec
[bwa_aln_core] refine gapped alignments... 7.21 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.02 sec
[bwa_aln_core] refine gapped alignments... 7.15 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.71 sec
[bwa_aln_core] refine gapped alignments... 7.28 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.18 sec
[bwa_aln_core] refine gapped alignments... 8.17 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.17 sec
[bwa_aln_core] refine gapped alignments... 7.95 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 50.09 sec
[bwa_aln_core] refine gapped alignments... 7.90 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.52 sec
[bwa_aln_core] refine gapped alignments... 6.77 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.12 sec
[bwa_aln_core] refine gapped alignments... 6.79 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.06 sec
[bwa_aln_core] refine gapped alignments... 6.84 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.08 sec
[bwa_aln_core] refine gapped alignments... 5.27 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.82 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.39 sec
[bwa_aln_core] refine gapped alignments... 4.83 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.24 sec
[bwa_aln_core] refine gapped alignments... 4.04 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.48 sec
[bwa_aln_core] refine gapped alignments... 3.98 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.51 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.73 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.67 sec
[bwa_aln_core] refine gapped alignments... 4.10 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.86 sec
[bwa_aln_core] refine gapped alignments... 4.23 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.51 sec
[bwa_aln_core] refine gapped alignments... 7.71 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.35 sec
[bwa_aln_core] refine gapped alignments... 6.50 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.06 sec
[bwa_aln_core] refine gapped alignments... 3.38 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.98 sec
[bwa_aln_core] refine gapped alignments... 4.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.93 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.12 sec
[bwa_aln_core] refine gapped alignments... 6.03 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.07 sec
[bwa_aln_core] refine gapped alignments... 5.44 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.56 sec
[bwa_aln_core] refine gapped alignments... 4.97 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.71 sec
[bwa_aln_core] refine gapped alignments... 5.33 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.82 sec
[bwa_aln_core] refine gapped alignments... 5.42 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.63 sec
[bwa_aln_core] refine gapped alignments... 5.00 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.84 sec
[bwa_aln_core] refine gapped alignments... 5.89 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.02 sec
[bwa_aln_core] refine gapped alignments... 5.98 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.58 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.55 sec
[bwa_aln_core] refine gapped alignments... 5.25 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.06 sec
[bwa_aln_core] refine gapped alignments... 8.13 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.10 sec
[bwa_aln_core] refine gapped alignments... 7.62 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.51 sec
[bwa_aln_core] refine gapped alignments... 6.71 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.71 sec
[bwa_aln_core] refine gapped alignments... 7.48 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.94 sec
[bwa_aln_core] refine gapped alignments... 6.29 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.67 sec
[bwa_aln_core] refine gapped alignments... 6.28 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.53 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.83 sec
[bwa_aln_core] refine gapped alignments... 5.72 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.66 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.34 sec
[bwa_aln_core] refine gapped alignments... 6.25 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.00 sec
[bwa_aln_core] refine gapped alignments... 5.22 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.57 sec
[bwa_aln_core] refine gapped alignments... 7.77 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.17 sec
[bwa_aln_core] refine gapped alignments... 6.99 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.51 sec
[bwa_aln_core] refine gapped alignments... 5.79 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.73 sec
[bwa_aln_core] refine gapped alignments... 6.65 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.90 sec
[bwa_aln_core] refine gapped alignments... 7.55 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.16 sec
[bwa_aln_core] refine gapped alignments... 6.58 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.66 sec
[bwa_aln_core] refine gapped alignments... 5.24 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.07 sec
[bwa_aln_core] refine gapped alignments... 7.05 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.20 sec
[bwa_aln_core] refine gapped alignments... 5.66 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.02 sec
[bwa_aln_core] refine gapped alignments... 7.27 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.73 sec
[bwa_aln_core] refine gapped alignments... 8.28 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.89 sec
[bwa_aln_core] refine gapped alignments... 6.88 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.71 sec
[bwa_aln_core] refine gapped alignments... 6.04 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.45 sec
[bwa_aln_core] refine gapped alignments... 6.21 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.18 sec
[bwa_aln_core] refine gapped alignments... 6.22 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.98 sec
[bwa_aln_core] refine gapped alignments... 6.18 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.73 sec
[bwa_aln_core] refine gapped alignments... 6.33 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.72 sec
[bwa_aln_core] refine gapped alignments... 6.34 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.34 sec
[bwa_aln_core] refine gapped alignments... 8.24 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.09 sec
[bwa_aln_core] refine gapped alignments... 8.13 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.30 sec
[bwa_aln_core] refine gapped alignments... 8.34 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.10 sec
[bwa_aln_core] refine gapped alignments... 8.01 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.09 sec
[bwa_aln_core] refine gapped alignments... 8.21 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.06 sec
[bwa_aln_core] refine gapped alignments... 8.04 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.15 sec
[bwa_aln_core] refine gapped alignments... 7.26 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.69 sec
[bwa_aln_core] refine gapped alignments... 7.91 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.96 sec
[bwa_aln_core] refine gapped alignments... 7.13 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.99 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.51 sec
[bwa_aln_core] refine gapped alignments... 1.98 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.83 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.15 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.12 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.18 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.83 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.05 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.84 sec
[bwa_aln_core] refine gapped alignments... 4.53 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.06 sec
[bwa_aln_core] refine gapped alignments... 3.81 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.34 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.11 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.72 sec
[bwa_aln_core] refine gapped alignments... 5.56 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.16 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.64 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 3.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.47 sec
[bwa_aln_core] refine gapped alignments... 0.89 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 2.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.31 sec
[bwa_aln_core] refine gapped alignments... 3.90 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.08 sec
[bwa_aln_core] refine gapped alignments... 4.35 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.08 sec
[bwa_aln_core] refine gapped alignments... 3.75 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.32 sec
[bwa_aln_core] refine gapped alignments... 3.36 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.82 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.85 sec
[bwa_aln_core] refine gapped alignments... 3.36 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.79 sec
[bwa_aln_core] refine gapped alignments... 3.32 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.81 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.23 sec
[bwa_aln_core] refine gapped alignments... 2.40 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.86 sec
[bwa_aln_core] refine gapped alignments... 2.15 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.56 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.85 sec
[bwa_aln_core] refine gapped alignments... 3.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.23 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.46 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.78 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.58 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.67 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.67 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.69 sec
[bwa_aln_core] refine gapped alignments... 2.13 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.27 sec
[bwa_aln_core] refine gapped alignments... 1.49 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.58 sec
[bwa_aln_core] refine gapped alignments... 1.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.98 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.92 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.53 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.41 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 1.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.38 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.28 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.15 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.21 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.02 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.94 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.23 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.85 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.72 sec
[bwa_aln_core] refine gapped alignments... 1.05 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.65 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.61 sec
[bwa_aln_core] refine gapped alignments... 1.07 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.68 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.27 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.50 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.85 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.04 sec
[bwa_aln_core] refine gapped alignments... 2.77 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.12 sec
[bwa_aln_core] refine gapped alignments... 2.21 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.17 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.00 sec
[bwa_aln_core] refine gapped alignments... 2.85 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.85 sec
[bwa_aln_core] refine gapped alignments... 2.98 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 1.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.10 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.09 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.19 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.04 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.18 sec
[bwa_aln_core] refine gapped alignments... 1.69 sec
[bwa_aln_core] print alignments... 0.26 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.28 sec
[bwa_aln_core] refine gapped alignments... 1.77 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.39 sec
[bwa_aln_core] refine gapped alignments... 1.53 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.77 sec
[bwa_aln_core] refine gapped alignments... 1.52 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.15 sec
[bwa_aln_core] refine gapped alignments... 1.57 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.25 sec
[bwa_aln_core] refine gapped alignments... 1.60 sec
[bwa_aln_core] print alignments... 0.27 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 1.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.11 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.32 sec
[bwa_aln_core] refine gapped alignments... 2.48 sec
[bwa_aln_core] print alignments... 0.29 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 1.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.54 sec
[bwa_aln_core] refine gapped alignments... 2.48 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.45 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.34 sec
[bwa_aln_core] refine gapped alignments... 2.78 sec
[bwa_aln_core] print alignments... 0.25 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.14 sec
[bwa_aln_core] refine gapped alignments... 3.31 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.47 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.51 sec
[bwa_aln_core] refine gapped alignments... 2.49 sec
[bwa_aln_core] print alignments... 0.28 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 1.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.17 sec
[bwa_aln_core] refine gapped alignments... 2.55 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.66 sec
[bwa_aln_core] refine gapped alignments... 2.44 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.67 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.68 sec
[bwa_aln_core] refine gapped alignments... 2.89 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.01 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.20 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.76 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.10 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.41 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.90 sec
[bwa_aln_core] refine gapped alignments... 2.81 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.59 sec
[bwa_aln_core] refine gapped alignments... 2.90 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.37 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.25 sec
[bwa_aln_core] refine gapped alignments... 2.85 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.00 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.52 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.37 sec
[bwa_aln_core] refine gapped alignments... 3.02 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.73 sec
[bwa_aln_core] refine gapped alignments... 3.02 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.99 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.83 sec
[bwa_aln_core] refine gapped alignments... 3.13 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.17 sec
[bwa_aln_core] refine gapped alignments... 2.84 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.10 sec
[bwa_aln_core] refine gapped alignments... 2.94 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.18 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.07 sec
[bwa_aln_core] refine gapped alignments... 4.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.52 sec
[bwa_aln_core] refine gapped alignments... 4.19 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.46 sec
[bwa_aln_core] refine gapped alignments... 3.88 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.12 sec
[bwa_aln_core] refine gapped alignments... 4.50 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.14 sec
[bwa_aln_core] refine gapped alignments... 2.73 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.34 sec
[bwa_aln_core] refine gapped alignments... 3.13 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.53 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.67 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.69 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 65536000 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.52 sec
[bwa_aln_core] refine gapped alignments... 3.54 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 65798144 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.66 sec
[bwa_aln_core] refine gapped alignments... 3.37 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 66060288 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.64 sec
[bwa_aln_core] refine gapped alignments... 3.41 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 66322432 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.95 sec
[bwa_aln_core] refine gapped alignments... 2.54 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 66584576 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.28 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 66846720 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.47 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 67108864 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.55 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 67371008 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.77 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 67633152 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.64 sec
[bwa_aln_core] refine gapped alignments... 3.67 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 67895296 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.48 sec
[bwa_aln_core] refine gapped alignments... 3.66 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 68157440 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.89 sec
[bwa_aln_core] refine gapped alignments... 4.01 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 68419584 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.07 sec
[bwa_aln_core] refine gapped alignments... 3.81 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 68681728 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.58 sec
[bwa_aln_core] refine gapped alignments... 3.62 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 68943872 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.30 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 69206016 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.46 sec
[bwa_aln_core] refine gapped alignments... 3.02 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 69468160 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.67 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 69730304 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.08 sec
[bwa_aln_core] refine gapped alignments... 2.80 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 69992448 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.68 sec
[bwa_aln_core] refine gapped alignments... 2.38 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 70254592 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.42 sec
[bwa_aln_core] refine gapped alignments... 1.84 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 70516736 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.30 sec
[bwa_aln_core] refine gapped alignments... 1.89 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.58 sec
[bwa_aln_core] refine gapped alignments... 1.87 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 71041024 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.08 sec
[bwa_aln_core] refine gapped alignments... 1.93 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 71303168 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.13 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 71565312 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.30 sec
[bwa_aln_core] refine gapped alignments... 1.86 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 71827456 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.30 sec
[bwa_aln_core] refine gapped alignments... 1.91 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 72089600 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.15 sec
[bwa_aln_core] refine gapped alignments... 1.85 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 72351744 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.11 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 72613888 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.79 sec
[bwa_aln_core] refine gapped alignments... 1.83 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 72876032 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.49 sec
[bwa_aln_core] refine gapped alignments... 2.17 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 73138176 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.01 sec
[bwa_aln_core] refine gapped alignments... 3.57 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 73400320 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.07 sec
[bwa_aln_core] refine gapped alignments... 3.04 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 73662464 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.13 sec
[bwa_aln_core] refine gapped alignments... 2.60 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 73924608 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.96 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 74186752 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.28 sec
[bwa_aln_core] refine gapped alignments... 1.96 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 74448896 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.19 sec
[bwa_aln_core] refine gapped alignments... 2.04 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 74711040 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.88 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 74973184 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.81 sec
[bwa_aln_core] refine gapped alignments... 2.29 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 75235328 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.04 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 75497472 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.64 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 75759616 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.08 sec
[bwa_aln_core] refine gapped alignments... 3.34 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76021760 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.88 sec
[bwa_aln_core] refine gapped alignments... 3.13 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76283904 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.62 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 76546048 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.59 sec
[bwa_aln_core] refine gapped alignments... 3.81 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 76808192 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.92 sec
[bwa_aln_core] refine gapped alignments... 3.70 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 77070336 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.95 sec
[bwa_aln_core] refine gapped alignments... 3.15 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 77332480 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.55 sec
[bwa_aln_core] refine gapped alignments... 3.01 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 77594624 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.93 sec
[bwa_aln_core] refine gapped alignments... 3.87 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 77856768 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.86 sec
[bwa_aln_core] refine gapped alignments... 3.79 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 78118912 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.64 sec
[bwa_aln_core] refine gapped alignments... 3.37 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 78381056 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.17 sec
[bwa_aln_core] refine gapped alignments... 3.30 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 78643200 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.09 sec
[bwa_aln_core] refine gapped alignments... 3.65 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 78905344 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.47 sec
[bwa_aln_core] refine gapped alignments... 3.35 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 79167488 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.16 sec
[bwa_aln_core] refine gapped alignments... 2.69 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 79429632 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.59 sec
[bwa_aln_core] refine gapped alignments... 2.76 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 79691776 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.78 sec
[bwa_aln_core] refine gapped alignments... 2.07 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 79953920 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.23 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 80216064 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.93 sec
[bwa_aln_core] refine gapped alignments... 3.90 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 80478208 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.07 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 80740352 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.32 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 81002496 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.39 sec
[bwa_aln_core] refine gapped alignments... 3.75 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 81264640 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.70 sec
[bwa_aln_core] refine gapped alignments... 3.16 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 81526784 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.85 sec
[bwa_aln_core] refine gapped alignments... 5.50 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 81788928 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.20 sec
[bwa_aln_core] refine gapped alignments... 2.23 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 82051072 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.41 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 82313216 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.65 sec
[bwa_aln_core] refine gapped alignments... 4.71 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 82575360 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.20 sec
[bwa_aln_core] refine gapped alignments... 3.09 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 82837504 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.37 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 83099648 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.09 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 83361792 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.86 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 83623936 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.41 sec
[bwa_aln_core] refine gapped alignments... 5.64 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 83886080 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.16 sec
[bwa_aln_core] refine gapped alignments... 4.57 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 84148224 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.84 sec
[bwa_aln_core] refine gapped alignments... 3.90 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 84410368 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.01 sec
[bwa_aln_core] refine gapped alignments... 7.98 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 84672512 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.18 sec
[bwa_aln_core] refine gapped alignments... 5.80 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 84934656 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.01 sec
[bwa_aln_core] refine gapped alignments... 3.17 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 85196800 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.75 sec
[bwa_aln_core] refine gapped alignments... 5.78 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 85458944 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.16 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 85721088 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.90 sec
[bwa_aln_core] refine gapped alignments... 3.41 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 85983232 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.82 sec
[bwa_aln_core] refine gapped alignments... 2.88 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 86245376 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.79 sec
[bwa_aln_core] refine gapped alignments... 2.87 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 86507520 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 37.67 sec
[bwa_aln_core] refine gapped alignments... 4.74 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 86769664 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.96 sec
[bwa_aln_core] refine gapped alignments... 6.66 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 87031808 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.64 sec
[bwa_aln_core] refine gapped alignments... 4.51 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 87293952 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.75 sec
[bwa_aln_core] refine gapped alignments... 4.80 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 87556096 sequences have been processed.
[bwa_read_seq] 0.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.84 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 87818240 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.59 sec
[bwa_aln_core] refine gapped alignments... 5.42 sec
[bwa_aln_core] print alignments... 0.05 sec
[bwa_aln_core] 87862603 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/ZF11/out/align/rep1/ZF11_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF11_allReps.fastq.gz
[main] Real time: 15690.350 sec; CPU: 15549.632 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/ZF11/out/align/rep1/ZF11_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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/ZF11/out/align/rep1/ZF11_allReps.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.bam | \
			    	sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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--------------------
4403 (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/ZF11/out/align/rep1/ZF11_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_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--------------------
15499 (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 00:10:07 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_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 00:10:07 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory)
INFO	2016-09-29 00:10:07	MarkDuplicates	Start of doWork freeMemory: 255390288; totalMemory: 257294336; maxMemory: 3817799680
INFO	2016-09-29 00:10:07	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-09-29 00:10:07	MarkDuplicates	Will retain up to 15149998 data points before spilling to disk.
WARNING	2016-09-29 00:10:07	AbstractDuplicateFindingAlgorithm	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836466.29916166'.  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 00:10:10	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:03s.  Time for last 1,000,000:    3s.  Last read position: chr1:64,323,528
INFO	2016-09-29 00:10:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:13	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:05s.  Time for last 1,000,000:    2s.  Last read position: chr1:120,523,234
INFO	2016-09-29 00:10:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:15	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    2s.  Last read position: chr1:161,840,504
INFO	2016-09-29 00:10:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:18	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:11s.  Time for last 1,000,000:    3s.  Last read position: chr2:4,838,316
INFO	2016-09-29 00:10:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:20	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    1s.  Last read position: chr2:34,768,117
INFO	2016-09-29 00:10:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:23	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:16s.  Time for last 1,000,000:    3s.  Last read position: chr2:85,015,743
INFO	2016-09-29 00:10:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:25	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    1s.  Last read position: chr2:128,135,130
INFO	2016-09-29 00:10:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:27	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    1s.  Last read position: chr2:163,616,766
INFO	2016-09-29 00:10:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:29	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr3:28,748,264
INFO	2016-09-29 00:10:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:32	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:25s.  Time for last 1,000,000:    3s.  Last read position: chr3:88,071,964
INFO	2016-09-29 00:10:32	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:34	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    1s.  Last read position: chr3:121,815,272
INFO	2016-09-29 00:10:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:36	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    1s.  Last read position: chr4:21,885,938
INFO	2016-09-29 00:10:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:38	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    1s.  Last read position: chr4:81,815,681
INFO	2016-09-29 00:10:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:40	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    1s.  Last read position: chr4:125,800,364
INFO	2016-09-29 00:10:40	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:43	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    3s.  Last read position: chr4:141,778,336
INFO	2016-09-29 00:10:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:52	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    8s.  Last read position: chr5:31,220,226
INFO	2016-09-29 00:10:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:54	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:00:47s.  Time for last 1,000,000:    2s.  Last read position: chr5:87,624,842
INFO	2016-09-29 00:10:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:56	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:    1s.  Last read position: chr5:121,724,088
INFO	2016-09-29 00:10:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:10:58	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    1s.  Last read position: chr5:144,435,388
INFO	2016-09-29 00:10:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:00	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    1s.  Last read position: chr6:48,087,549
INFO	2016-09-29 00:11:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:02	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    2s.  Last read position: chr6:91,748,453
INFO	2016-09-29 00:11:02	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:04	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:00:57s.  Time for last 1,000,000:    1s.  Last read position: chr6:133,995,521
INFO	2016-09-29 00:11:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:06	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:    1s.  Last read position: chr7:28,302,331
INFO	2016-09-29 00:11:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:10	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    3s.  Last read position: chr7:75,428,750
INFO	2016-09-29 00:11:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:11	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:01:04s.  Time for last 1,000,000:    1s.  Last read position: chr7:113,544,026
INFO	2016-09-29 00:11:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:13	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:01:06s.  Time for last 1,000,000:    2s.  Last read position: chr7:144,159,410
INFO	2016-09-29 00:11:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:15	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:01:08s.  Time for last 1,000,000:    1s.  Last read position: chr8:64,135,892
INFO	2016-09-29 00:11:15	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:17	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:    1s.  Last read position: chr8:99,947,241
INFO	2016-09-29 00:11:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:19	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    2s.  Last read position: chr8:127,272,734
INFO	2016-09-29 00:11:19	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:23	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    3s.  Last read position: chr9:51,232,064
INFO	2016-09-29 00:11:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:31	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:01:23s.  Time for last 1,000,000:    7s.  Last read position: chr9:80,252,484
INFO	2016-09-29 00:11:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:33	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:    2s.  Last read position: chr9:119,254,406
INFO	2016-09-29 00:11:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:35	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:01:27s.  Time for last 1,000,000:    1s.  Last read position: chr10:43,963,097
INFO	2016-09-29 00:11:35	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:37	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:01:29s.  Time for last 1,000,000:    1s.  Last read position: chr10:80,651,235
INFO	2016-09-29 00:11:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:39	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:01:32s.  Time for last 1,000,000:    2s.  Last read position: chr10:121,194,280
INFO	2016-09-29 00:11:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:41	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:01:33s.  Time for last 1,000,000:    1s.  Last read position: chr11:33,182,962
INFO	2016-09-29 00:11:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:43	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:01:36s.  Time for last 1,000,000:    2s.  Last read position: chr11:68,755,199
INFO	2016-09-29 00:11:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:46	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    3s.  Last read position: chr11:88,583,696
INFO	2016-09-29 00:11:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:48	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:01:41s.  Time for last 1,000,000:    2s.  Last read position: chr11:107,135,869
INFO	2016-09-29 00:11:48	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:50	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:    1s.  Last read position: chr12:16,648,249
INFO	2016-09-29 00:11:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:52	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:01:45s.  Time for last 1,000,000:    2s.  Last read position: chr12:80,763,125
INFO	2016-09-29 00:11:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:54	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:    1s.  Last read position: chr12:116,289,051
INFO	2016-09-29 00:11:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:57	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:01:49s.  Time for last 1,000,000:    2s.  Last read position: chr13:48,587,825
INFO	2016-09-29 00:11:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:11:58	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:01:51s.  Time for last 1,000,000:    1s.  Last read position: chr13:97,241,157
INFO	2016-09-29 00:11:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:00	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:01:53s.  Time for last 1,000,000:    1s.  Last read position: chr14:32,422,155
INFO	2016-09-29 00:12:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:09	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:02:01s.  Time for last 1,000,000:    8s.  Last read position: chr14:75,641,095
INFO	2016-09-29 00:12:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:10	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:02:03s.  Time for last 1,000,000:    1s.  Last read position: chr15:30,782,231
INFO	2016-09-29 00:12:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:13	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:02:05s.  Time for last 1,000,000:    2s.  Last read position: chr15:79,255,318
INFO	2016-09-29 00:12:13	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:14	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:02:07s.  Time for last 1,000,000:    1s.  Last read position: chr15:102,525,185
INFO	2016-09-29 00:12:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:16	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:02:09s.  Time for last 1,000,000:    2s.  Last read position: chr16:34,667,337
INFO	2016-09-29 00:12:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:18	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:02:11s.  Time for last 1,000,000:    1s.  Last read position: chr16:94,551,919
INFO	2016-09-29 00:12:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:20	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:    1s.  Last read position: chr17:31,611,859
INFO	2016-09-29 00:12:20	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:22	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    1s.  Last read position: chr17:62,430,888
INFO	2016-09-29 00:12:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:24	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    1s.  Last read position: chr18:24,155,404
INFO	2016-09-29 00:12:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:26	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:02:18s.  Time for last 1,000,000:    1s.  Last read position: chr18:69,704,780
INFO	2016-09-29 00:12:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:02:20s.  Time for last 1,000,000:    1s.  Last read position: chr19:19,717,519
INFO	2016-09-29 00:12:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:29	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:02:22s.  Time for last 1,000,000:    1s.  Last read position: chr19:56,073,727
INFO	2016-09-29 00:12:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:34	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:    4s.  Last read position: chrX:146,810,338
INFO	2016-09-29 00:12:34	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-09-29 00:12:34	MarkDuplicates	Read 58248940 records. 0 pairs never matched.
INFO	2016-09-29 00:12:40	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2787283624; totalMemory: 2873950208; maxMemory: 3817799680
INFO	2016-09-29 00:12:40	MarkDuplicates	Will retain up to 119306240 duplicate indices before spilling to disk.
INFO	2016-09-29 00:12:40	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-09-29 00:12:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-09-29 00:12:52	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-09-29 00:12:54	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1887203680; totalMemory: 2866479104; maxMemory: 3817799680
INFO	2016-09-29 00:12:54	MarkDuplicates	Marking 28041654 records as duplicates.
INFO	2016-09-29 00:12:54	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2016-09-29 00:14:12	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:18s.  Time for last 10,000,000:   78s.  Last read position: chr3:88,071,964
INFO	2016-09-29 00:15:30	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:02:35s.  Time for last 10,000,000:   77s.  Last read position: chr6:48,087,549
INFO	2016-09-29 00:16:47	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:03:53s.  Time for last 10,000,000:   77s.  Last read position: chr9:51,232,064
INFO	2016-09-29 00:18:04	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:10s.  Time for last 10,000,000:   77s.  Last read position: chr12:16,648,249
INFO	2016-09-29 00:19:22	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:06:28s.  Time for last 10,000,000:   77s.  Last read position: chr16:34,667,337
INFO	2016-09-29 00:20:27	MarkDuplicates	Before output close freeMemory: 2936992256; totalMemory: 2966749184; maxMemory: 3817799680
INFO	2016-09-29 00:20:28	MarkDuplicates	After output close freeMemory: 2936991416; totalMemory: 2966749184; maxMemory: 3817799680
[Thu Sep 29 00:20:28 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 10.36 minutes.
Runtime.totalMemory()=2966749184

 

 
# 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/ZF11/out/align/rep1/ZF11_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.bam

# SYS command. line 153

 sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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/ZF11/out/qc/rep1/ZF11_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--------------------
9775 (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/ZF11/out/align/rep1/ZF11_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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--------------------
40931 (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/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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--------------------
41088 (process ID) old priority 0, new priority 10
Waiting for 8 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/ZF11/out/align/rep1/ZF11_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/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_allReps.nodup.

# SYS command. line 260

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_allReps.nodup.pr1.tagAlign.gz

# SYS command. line 261

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_allReps.nodup.00

# SYS command. line 262

 gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr2/ZF11_allReps.nodup.pr2.tagAlign.gz

# SYS command. line 263

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/pseudo_reps/rep1/pr1/ZF11_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--------------------
27094 (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/ZF11/out/align/rep1/ZF11_allReps.nodup.15M.tagAlign.gz -p=4 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.qc 

# SYS command. line 219

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.qc.tmp

# SYS command. line 220

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_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--------------------
5815 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_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/ZF11/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/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.15M.tagAlign.gz 
opened /tmp/9772.1.q/RtmpPUFH7O/ZF11_allReps.nodup.15M.tagAlign16fe63869836
done. read 15000000 fragments
ChIP data read length 36 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1949332 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.288441215878854 
Top 3 estimates for fragment length 125 
Window half size 375 
Phantom peak location 40 
Phantom peak Correlation 0.2663732 
Normalized Strand cross-correlation coefficient (NSC) 1.479693 
Relative Strand Cross correlation Coefficient (RSC) 1.308903 
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/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1 -speak=125 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore

# SYS command. line 67

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_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/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 69

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz

# SYS command. line 71

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf

# SYS command. line 74

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi

# SYS command. line 77

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_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
 

   
--------------------Stdout--------------------
42051 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 125 
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/ZF11/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_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/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz 
opened /tmp/9773.1.q/RtmpQBUykP/ZF11_allReps.nodup.tagAligna48578f50908
done. read 30207286 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz 
opened /tmp/9773.1.q/RtmpQBUykP/mousePrimaryBCellInput.nodup.tagAligna485bd11e77
done. read 15331612 fragments
Control data read length 36 
Calculating peak characteristics
Minimum cross-correlation value 0.3042838 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.450586479744112 
Top 3 estimates for fragment length 125 
Window half size 375 
Phantom peak location 55 
Phantom peak Correlation 0.4259703 
Normalized Strand cross-correlation coefficient (NSC) 1.48081 
Relative Strand Cross correlation Coefficient (RSC) 1.202292 
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= 0.7116029  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 1.405278  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00003 
Detected 1038258 peaks 

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 23 warnings (use warnings() to see them)

 

 
# 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 209

 echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/ZF11_IDR_final.qc

# SYS command. line 210

 echo -e "0\t""0\tN/A\tN/A\tNaN\tNaN\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/ZF11_IDR_final.qc

# SYS command. line 212

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

   
--------------------Stdout--------------------
33316 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

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

 

 
# SYS command. line 98

 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 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.svg" # to suppress dot font error (exit code=1)
 

   
--------------------Stdout--------------------
33440 (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 325

 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 326

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/qc/rep1/ZF11_allReps.nodup.15M.cc.plot.pdf
 

   
--------------------Stdout--------------------
33478 (process ID) old priority 0, new priority 10

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