| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20160928_164747_977 |
| Start time | 2016-09-28 16:47:47 |
| Run time | 22:51:41.955 |
| Tasks executed | 16 |
| Tasks failed | 1 |
| Tasks failed names | spp rep1 |
| Arguments* | [-title, ZF6, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF6_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20160928_164747_977/task.callpeak_spp.spp_rep1.line_54.id_25 |
| thread_42 | thread_Root | chipseq.bds.20160928_164747_977_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20160928_164747_977_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12 chipseq.bds.20160928_164747_977_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13 chipseq.bds.20160928_164747_977_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14 chipseq.bds.20160928_164747_977_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20160928_164747_977_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16 |
| thread_41 | thread_Root | chipseq.bds.20160928_164747_977_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20160928_164747_977_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20160928_164747_977_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# 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/ZF6_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_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-------------------- 12276 (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... 38.38 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... 36.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.64 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.44 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.76 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.27 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.44 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.60 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 2359296 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... 0.07 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.76 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 2883584 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... 0.05 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.76 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... 40.19 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.32 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.75 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.53 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... 41.92 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... 42.94 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.14 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... 42.83 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... 43.29 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.33 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.11 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.62 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.22 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.37 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.06 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.06 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.61 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.16 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... 44.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.01 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.35 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.25 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.70 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.93 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.07 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.15 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.11 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... 43.70 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... 42.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.15 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15466496 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] 15728640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.87 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.42 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... 43.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.88 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.48 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.36 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.14 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.31 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.55 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.15 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.70 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.11 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.73 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.25 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.35 sec [bwa_aln_core] write to the disk... 0.12 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.96 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.57 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.08 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.54 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.48 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.97 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.01 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.79 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... 43.48 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.63 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.77 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... 42.21 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... 42.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.64 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 29097984 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... 0.06 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.01 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29884416 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... 0.09 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.42 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.25 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.03 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.77 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... 44.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.70 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.94 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.03 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.98 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.28 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.62 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.19 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.14 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.01 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.08 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.37 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.20 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 36700160 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] 36962304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.08 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.51 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 37748736 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] 38010880 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.58 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.48 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.94 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.91 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.04 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.40 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.78 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.03 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.13 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 42205184 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] 42467328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.05 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 42729472 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... 0.05 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.99 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.58 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.46 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 0.1% 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] 44826624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.39 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.07 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.26 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.78 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.86 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.89 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 47185920 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... 0.05 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.13 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.50 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.09 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.43 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.33 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.12 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.03 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.91 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.63 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.60 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.01 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.66 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.63 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.18 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.24 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 54525952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 54788096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 55050240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 55312384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.34 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 55574528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.78 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 55836672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.42 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 56098816 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... 0.06 sec [bwa_aln_core] 56360960 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 56623104 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 56885248 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.06 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 57147392 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.61 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 57409536 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.54 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 57671680 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.09 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 57933824 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 58195968 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.95 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 58458112 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 58720256 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 58982400 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.98 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 59244544 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.76 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 59506688 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.31 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 59768832 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... 0.05 sec [bwa_aln_core] 60030976 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.39 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 60293120 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 60555264 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.36 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 60817408 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... 0.06 sec [bwa_aln_core] 61079552 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.29 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 61341696 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 61603840 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.57 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61865984 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... 0.08 sec [bwa_aln_core] 62128128 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 62390272 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 62652416 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.80 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 62914560 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 63176704 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.67 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 63438848 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 63700992 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 63963136 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 64225280 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 64487424 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.65 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 64749568 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 65011712 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.38 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 65273856 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 65536000 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 65798144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66060288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.12 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... 35.93 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 66584576 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66846720 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.19 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 67108864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 67371008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.92 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 67633152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.13 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 67895296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.22 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... 35.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 68419584 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 68681728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.56 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 68943872 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.75 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... 36.75 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 69468160 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 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... 36.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 69992448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.48 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 70254592 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.77 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 70516736 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 70778880 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 71041024 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.93 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 71303168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.75 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... 36.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 71827456 sequences have been processed. [bwa_read_seq] 0.2% 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] 72089600 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.38 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 72351744 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 72613888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 72876032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.14 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... 38.16 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... 37.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 73662464 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 73924608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.82 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 74186752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.88 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 74448896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 74711040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 74973184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 75235328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 75497472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 75759616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 76021760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.11 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 76283904 sequences have been processed. [bwa_read_seq] 0.2% 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] 76546048 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... 0.06 sec [bwa_aln_core] 76808192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.55 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 77070336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 77332480 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.89 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 77594624 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.00 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 77856768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.71 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78118912 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 110.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78381056 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 78643200 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 78905344 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 79167488 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 79429632 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 79691776 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 79953920 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 80216064 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 80478208 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.09 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 80740352 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.47 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 81002496 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 81264640 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.77 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 81526784 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 81788928 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 82051072 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.19 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 82313216 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 82575360 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 82837504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 83099648 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 83361792 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 83623936 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.51 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 83886080 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 84148224 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.90 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 84410368 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 84672512 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.50 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 84934656 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.55 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 85196800 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.18 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 85458944 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 85721088 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.20 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 85983232 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 86245376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.99 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 86507520 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.02 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 86769664 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.24 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 87031808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.90 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 87293952 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.68 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 87556096 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.12 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 87818240 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.94 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 88080384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.58 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 88342528 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.40 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 88604672 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.85 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 88866816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 89128960 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 89391104 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.94 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 89653248 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 89915392 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.08 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 90177536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 90439680 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 90701824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 90963968 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.58 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 91226112 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 91488256 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.61 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 91750400 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 101.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 92012544 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 92274688 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 92536832 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 92798976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.53 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 93061120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 93323264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 93585408 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.05 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 93847552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 94109696 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 103.75 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 94371840 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.55 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 94633984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94896128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.24 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 95158272 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 106.03 sec [bwa_aln_core] write to the disk... 0.12 sec [bwa_aln_core] 95420416 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 104.73 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 95682560 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.20 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 95944704 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.35 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 96206848 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.03 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 96468992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 120.54 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 96731136 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 96993280 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 121.13 sec [bwa_aln_core] write to the disk... 0.12 sec [bwa_aln_core] 97255424 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 116.69 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 97517568 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.46 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 97779712 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 106.35 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 98041856 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.34 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 98304000 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.53 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 98566144 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.21 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 98828288 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.71 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 99090432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99352576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 99614720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99876864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.91 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 100139008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 100401152 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.75 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 100663296 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 100925440 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 101187584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 101449728 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.20 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 101711872 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.97 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 101974016 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 102236160 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.36 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 102498304 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.79 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 102760448 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 103022592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.23 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 103284736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 103546880 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 103809024 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 104071168 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 104333312 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 104595456 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.56 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 104857600 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 105119744 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.13 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 105381888 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 105644032 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.37 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 105906176 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 106168320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.70 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 106430464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.34 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 106692608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.10 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 106954752 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 107216896 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 107479040 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.72 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 107741184 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.94 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 108003328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.88 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 108265472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.65 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 108527616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.72 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 108789760 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.22 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 109051904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.96 sec [bwa_aln_core] write to the disk... 0.12 sec [bwa_aln_core] 109314048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.07 sec [bwa_aln_core] write to the disk... 0.10 sec [bwa_aln_core] 109576192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 109838336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.42 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 110100480 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.84 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 110362624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.28 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 110624768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.53 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 110886912 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.41 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 111149056 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.75 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 111411200 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.26 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 111673344 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.80 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 111935488 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 112197632 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 112459776 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 112721920 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 112984064 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 113246208 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.86 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 113508352 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 113770496 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.72 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 114023882 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/ZF6_allReps.fastq.gz [main] Real time: 6837.002 sec; CPU: 25495.020 sec | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/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-------------------- 4840 (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... 29.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.55 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... 27.42 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... 27.27 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.21 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.31 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.06 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... 27.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.17 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... 28.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.46 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... 27.96 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... 27.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.10 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.02 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.94 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.11 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.93 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.15 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... 27.03 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... 27.06 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... 30.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.32 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... 27.32 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... 27.28 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... 27.23 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.18 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... 27.24 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... 27.28 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... 27.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.25 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... 27.26 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.39 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... 27.58 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.47 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.70 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... 27.65 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.61 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... 27.48 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.50 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... 27.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.58 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... 27.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.46 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... 27.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.21 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.73 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... 28.60 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.39 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.91 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... 28.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.09 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... 28.06 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... 27.79 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... 29.58 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... 30.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.07 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... 28.08 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.39 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... 27.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.41 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... 27.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.52 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... 27.43 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 7.68 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: 2558.721 sec; CPU: 2559.880 sec | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/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/ZF6/out/align/ctl1/mousePrimaryBCellInput.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/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-------------------- 3607 (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... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.51 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.64 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.65 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.58 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.75 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.64 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.52 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.58 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.61 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.60 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.59 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.61 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.55 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.61 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.55 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% 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... 0.35 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.61 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.54 sec [bwa_aln_core] refine gapped alignments... 0.35 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... 2.84 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.86 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.83 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.86 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.86 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.39 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... 2.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% 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... 0.43 sec [bwa_aln_core] 12058624 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... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.82 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 14942208 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... 0.36 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.94 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.83 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 16252928 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... 0.37 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.61 sec [bwa_aln_core] refine gapped alignments... 0.49 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... 3.56 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.33 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.38 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.51 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.35 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... 3.39 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.49 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.37 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.31 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.09 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.31 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.05 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.15 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.21 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.93 sec [bwa_aln_core] refine gapped alignments... 0.45 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... 4.02 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.84 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.59 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.78 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.63 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.06 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.10 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/ZF6/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz [main] Real time: 451.950 sec; CPU: 374.304 sec | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 11032 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/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/ZF6/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/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-------------------- 11826 (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 17:49:13 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/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 17:49:13 PDT 2016] Executing as imk1@surya on Linux 4.2.0-27-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory) INFO 2016-09-28 17:49:13 MarkDuplicates Start of doWork freeMemory: 255390112; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-28 17:49:13 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-28 17:49:13 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. INFO 2016-09-28 17:49:19 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:174,151,470 INFO 2016-09-28 17:49:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:26 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 6s. Last read position: chr2:135,780,411 INFO 2016-09-28 17:49:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:34 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 8s. Last read position: chr3:122,530,375 INFO 2016-09-28 17:49:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:37 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr4:135,044,888 INFO 2016-09-28 17:49:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:43 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 6s. Last read position: chr5:135,067,778 INFO 2016-09-28 17:49:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:48 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 5s. Last read position: chr6:144,681,933 INFO 2016-09-28 17:49:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:51 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr8:12,749,386 INFO 2016-09-28 17:49:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:54 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr9:42,425,131 INFO 2016-09-28 17:49:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:49:59 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 4s. Last read position: chr10:69,658,983 INFO 2016-09-28 17:49:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:02 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr11:86,536,377 INFO 2016-09-28 17:50:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:05 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr13:6,026,344 INFO 2016-09-28 17:50:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:10 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 5s. Last read position: chr14:54,434,282 INFO 2016-09-28 17:50:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:13 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr15:98,839,731 INFO 2016-09-28 17:50:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:16 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr17:62,456,013 INFO 2016-09-28 17:50:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:19 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr19:38,585,732 INFO 2016-09-28 17:50:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:50:27 MarkDuplicates Read 15489502 records. 0 pairs never matched. INFO 2016-09-28 17:50:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 2366924592; totalMemory: 2453405696; maxMemory: 3817799680 INFO 2016-09-28 17:50:28 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-28 17:50:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-28 17:50:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-28 17:50:32 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-28 17:50:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 1946859456; totalMemory: 2922971136; maxMemory: 3817799680 INFO 2016-09-28 17:50:32 MarkDuplicates Marking 157890 records as duplicates. INFO 2016-09-28 17:50:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-28 17:51:57 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 84s. Last read position: chr11:86,536,377 INFO 2016-09-28 17:52:44 MarkDuplicates Before output close freeMemory: 2900049680; totalMemory: 2928279552; maxMemory: 3817799680 INFO 2016-09-28 17:52:44 MarkDuplicates After output close freeMemory: 2927180744; totalMemory: 2955411456; maxMemory: 3817799680 [Wed Sep 28 17:52:44 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 3.52 minutes. Runtime.totalMemory()=2955411456 | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/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+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/ctl1/mousePrimaryBCellInput.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 12426 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# 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 $$
# SYS command. line 509
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 13110 (process ID) old priority 0, new priority 10 Waiting for 30 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# 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/ZF6/out/align/rep1/ZF6_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF6_allReps.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.bam
# SYS command. line 149
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_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-------------------- 6551 (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... 29.07 sec [bwa_aln_core] refine gapped alignments... 4.40 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.34 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.77 sec [bwa_aln_core] refine gapped alignments... 4.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.22 sec [bwa_aln_core] refine gapped alignments... 4.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.91 sec [bwa_aln_core] refine gapped alignments... 4.99 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.09 sec [bwa_aln_core] refine gapped alignments... 4.38 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.65 sec [bwa_aln_core] refine gapped alignments... 4.37 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.49 sec [bwa_aln_core] refine gapped alignments... 4.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.34 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.28 sec [bwa_aln_core] refine gapped alignments... 2.26 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.94 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.20 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.42 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.22 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.07 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.18 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.38 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.12 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.26 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.82 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.44 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.43 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.15 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.32 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.35 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.08 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.30 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.73 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.95 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.15 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.13 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.25 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.94 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.92 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.25 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.22 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.56 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.44 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.46 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.54 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.39 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.33 sec [bwa_aln_core] refine gapped alignments... 4.14 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.77 sec [bwa_aln_core] refine gapped alignments... 3.20 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.99 sec [bwa_aln_core] refine gapped alignments... 3.20 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.17 sec [bwa_aln_core] refine gapped alignments... 3.78 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.21 sec [bwa_aln_core] refine gapped alignments... 1.05 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.45 sec [bwa_aln_core] refine gapped alignments... 1.17 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.50 sec [bwa_aln_core] refine gapped alignments... 2.23 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.40 sec [bwa_aln_core] refine gapped alignments... 3.29 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.40 sec [bwa_aln_core] refine gapped alignments... 3.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.23 sec [bwa_aln_core] refine gapped alignments... 1.36 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.61 sec [bwa_aln_core] refine gapped alignments... 2.07 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.21 sec [bwa_aln_core] refine gapped alignments... 1.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.14 sec [bwa_aln_core] refine gapped alignments... 2.17 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.08 sec [bwa_aln_core] refine gapped alignments... 1.29 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.95 sec [bwa_aln_core] refine gapped alignments... 1.50 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.53 sec [bwa_aln_core] refine gapped alignments... 3.12 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.58 sec [bwa_aln_core] refine gapped alignments... 1.04 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.68 sec [bwa_aln_core] refine gapped alignments... 2.63 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.61 sec [bwa_aln_core] refine gapped alignments... 0.94 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.37 sec [bwa_aln_core] refine gapped alignments... 2.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.80 sec [bwa_aln_core] refine gapped alignments... 3.69 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.72 sec [bwa_aln_core] refine gapped alignments... 2.72 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.83 sec [bwa_aln_core] refine gapped alignments... 2.85 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.84 sec [bwa_aln_core] refine gapped alignments... 3.15 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.82 sec [bwa_aln_core] refine gapped alignments... 2.90 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.72 sec [bwa_aln_core] refine gapped alignments... 1.03 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.24 sec [bwa_aln_core] refine gapped alignments... 4.61 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.61 sec [bwa_aln_core] refine gapped alignments... 3.47 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.28 sec [bwa_aln_core] refine gapped alignments... 2.09 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.62 sec [bwa_aln_core] refine gapped alignments... 4.86 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.33 sec [bwa_aln_core] refine gapped alignments... 3.55 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.76 sec [bwa_aln_core] refine gapped alignments... 5.31 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.71 sec [bwa_aln_core] refine gapped alignments... 2.42 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.39 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.55 sec [bwa_aln_core] refine gapped alignments... 2.47 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.58 sec [bwa_aln_core] refine gapped alignments... 2.46 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.61 sec [bwa_aln_core] refine gapped alignments... 4.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.96 sec [bwa_aln_core] refine gapped alignments... 5.37 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.82 sec [bwa_aln_core] refine gapped alignments... 4.73 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.60 sec [bwa_aln_core] refine gapped alignments... 4.97 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.26 sec [bwa_aln_core] refine gapped alignments... 3.02 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.34 sec [bwa_aln_core] refine gapped alignments... 4.86 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.82 sec [bwa_aln_core] refine gapped alignments... 2.99 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.71 sec [bwa_aln_core] refine gapped alignments... 2.99 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.69 sec [bwa_aln_core] refine gapped alignments... 3.08 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.68 sec [bwa_aln_core] refine gapped alignments... 4.25 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... 31.49 sec [bwa_aln_core] refine gapped alignments... 4.98 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.06 sec [bwa_aln_core] refine gapped alignments... 6.14 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.30 sec [bwa_aln_core] refine gapped alignments... 4.88 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.03 sec [bwa_aln_core] refine gapped alignments... 3.13 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.99 sec [bwa_aln_core] refine gapped alignments... 4.36 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.26 sec [bwa_aln_core] refine gapped alignments... 3.04 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.31 sec [bwa_aln_core] refine gapped alignments... 3.06 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.46 sec [bwa_aln_core] refine gapped alignments... 4.67 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.50 sec [bwa_aln_core] refine gapped alignments... 4.93 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.70 sec [bwa_aln_core] refine gapped alignments... 2.18 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.72 sec [bwa_aln_core] refine gapped alignments... 5.46 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.37 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.10 sec [bwa_aln_core] refine gapped alignments... 2.60 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.07 sec [bwa_aln_core] refine gapped alignments... 1.79 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.16 sec [bwa_aln_core] refine gapped alignments... 1.77 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.33 sec [bwa_aln_core] refine gapped alignments... 1.80 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.10 sec [bwa_aln_core] refine gapped alignments... 2.19 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.14 sec [bwa_aln_core] refine gapped alignments... 5.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 27262976 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... 1.64 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.12 sec [bwa_aln_core] refine gapped alignments... 3.64 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.11 sec [bwa_aln_core] refine gapped alignments... 4.88 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.87 sec [bwa_aln_core] refine gapped alignments... 3.71 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.10 sec [bwa_aln_core] refine gapped alignments... 2.08 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.41 sec [bwa_aln_core] refine gapped alignments... 1.33 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... 31.47 sec [bwa_aln_core] refine gapped alignments... 3.87 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.11 sec [bwa_aln_core] refine gapped alignments... 3.73 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.88 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.61 sec [bwa_aln_core] refine gapped alignments... 4.33 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.31 sec [bwa_aln_core] refine gapped alignments... 1.31 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.41 sec [bwa_aln_core] refine gapped alignments... 4.96 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.45 sec [bwa_aln_core] refine gapped alignments... 5.72 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.36 sec [bwa_aln_core] refine gapped alignments... 4.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.32 sec [bwa_aln_core] refine gapped alignments... 3.99 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 31195136 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... 4.87 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.11 sec [bwa_aln_core] refine gapped alignments... 3.94 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.38 sec [bwa_aln_core] refine gapped alignments... 4.65 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.45 sec [bwa_aln_core] refine gapped alignments... 1.30 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.56 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 32505856 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... 3.95 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.03 sec [bwa_aln_core] refine gapped alignments... 1.86 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.57 sec [bwa_aln_core] refine gapped alignments... 4.33 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.78 sec [bwa_aln_core] refine gapped alignments... 1.41 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.91 sec [bwa_aln_core] refine gapped alignments... 2.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.43 sec [bwa_aln_core] refine gapped alignments... 5.33 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.07 sec [bwa_aln_core] refine gapped alignments... 3.69 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.50 sec [bwa_aln_core] refine gapped alignments... 3.58 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.91 sec [bwa_aln_core] refine gapped alignments... 1.83 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.20 sec [bwa_aln_core] refine gapped alignments... 1.95 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.07 sec [bwa_aln_core] refine gapped alignments... 4.24 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.16 sec [bwa_aln_core] refine gapped alignments... 2.98 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.13 sec [bwa_aln_core] refine gapped alignments... 1.84 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.09 sec [bwa_aln_core] refine gapped alignments... 5.94 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.83 sec [bwa_aln_core] refine gapped alignments... 1.65 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 36438016 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... 5.82 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.73 sec [bwa_aln_core] refine gapped alignments... 1.80 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.75 sec [bwa_aln_core] refine gapped alignments... 1.88 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.82 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.07 sec [bwa_aln_core] refine gapped alignments... 0.79 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.00 sec [bwa_aln_core] refine gapped alignments... 2.55 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.73 sec [bwa_aln_core] refine gapped alignments... 2.93 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.64 sec [bwa_aln_core] refine gapped alignments... 1.07 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.05 sec [bwa_aln_core] refine gapped alignments... 1.50 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.43 sec [bwa_aln_core] refine gapped alignments... 5.75 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.24 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.97 sec [bwa_aln_core] refine gapped alignments... 3.50 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.50 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.64 sec [bwa_aln_core] refine gapped alignments... 3.45 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.99 sec [bwa_aln_core] refine gapped alignments... 5.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.33 sec [bwa_aln_core] refine gapped alignments... 2.52 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.15 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.82 sec [bwa_aln_core] refine gapped alignments... 2.28 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.19 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.87 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.32 sec [bwa_aln_core] refine gapped alignments... 0.81 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.88 sec [bwa_aln_core] refine gapped alignments... 1.15 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.11 sec [bwa_aln_core] refine gapped alignments... 2.82 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.77 sec [bwa_aln_core] refine gapped alignments... 2.71 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.61 sec [bwa_aln_core] refine gapped alignments... 2.29 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.37 sec [bwa_aln_core] refine gapped alignments... 2.16 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.36 sec [bwa_aln_core] refine gapped alignments... 1.76 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.87 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.72 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.56 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.11 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.70 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.16 sec [bwa_aln_core] refine gapped alignments... 3.01 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.66 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.93 sec [bwa_aln_core] refine gapped alignments... 3.26 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.77 sec [bwa_aln_core] refine gapped alignments... 2.52 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.73 sec [bwa_aln_core] refine gapped alignments... 2.51 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.81 sec [bwa_aln_core] refine gapped alignments... 2.60 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.38 sec [bwa_aln_core] refine gapped alignments... 2.49 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.42 sec [bwa_aln_core] refine gapped alignments... 2.49 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.47 sec [bwa_aln_core] refine gapped alignments... 2.28 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.15 sec [bwa_aln_core] refine gapped alignments... 2.17 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.55 sec [bwa_aln_core] refine gapped alignments... 2.18 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.40 sec [bwa_aln_core] refine gapped alignments... 2.14 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.97 sec [bwa_aln_core] refine gapped alignments... 3.84 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.06 sec [bwa_aln_core] refine gapped alignments... 4.53 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.23 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.62 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.47 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.76 sec [bwa_aln_core] refine gapped alignments... 3.31 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.83 sec [bwa_aln_core] refine gapped alignments... 3.25 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.60 sec [bwa_aln_core] refine gapped alignments... 2.08 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.99 sec [bwa_aln_core] refine gapped alignments... 1.50 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.71 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.17 sec [bwa_aln_core] refine gapped alignments... 3.41 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.65 sec [bwa_aln_core] refine gapped alignments... 1.98 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.55 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.39 sec [bwa_aln_core] refine gapped alignments... 3.31 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.01 sec [bwa_aln_core] refine gapped alignments... 4.23 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.04 sec [bwa_aln_core] refine gapped alignments... 3.72 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.77 sec [bwa_aln_core] refine gapped alignments... 2.70 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.15 sec [bwa_aln_core] refine gapped alignments... 3.48 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.03 sec [bwa_aln_core] refine gapped alignments... 2.04 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.32 sec [bwa_aln_core] refine gapped alignments... 2.18 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.56 sec [bwa_aln_core] refine gapped alignments... 2.46 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.03 sec [bwa_aln_core] refine gapped alignments... 3.97 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.53 sec [bwa_aln_core] refine gapped alignments... 2.59 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.67 sec [bwa_aln_core] refine gapped alignments... 2.63 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.82 sec [bwa_aln_core] refine gapped alignments... 1.99 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 54525952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.38 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 54788096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.06 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 55050240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.61 sec [bwa_aln_core] refine gapped alignments... 1.17 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 55312384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.29 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 55574528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.66 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 55836672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.59 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 56098816 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.56 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 56360960 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.35 sec [bwa_aln_core] refine gapped alignments... 3.36 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 56623104 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.15 sec [bwa_aln_core] refine gapped alignments... 1.08 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 56885248 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.31 sec [bwa_aln_core] refine gapped alignments... 3.15 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 57147392 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.25 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 57409536 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.02 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 57671680 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.39 sec [bwa_aln_core] refine gapped alignments... 2.61 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 57933824 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.92 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 58195968 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.93 sec [bwa_aln_core] refine gapped alignments... 2.91 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 58458112 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.96 sec [bwa_aln_core] refine gapped alignments... 2.56 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 58720256 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.12 sec [bwa_aln_core] refine gapped alignments... 2.59 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 58982400 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.88 sec [bwa_aln_core] refine gapped alignments... 2.49 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 59244544 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.96 sec [bwa_aln_core] refine gapped alignments... 2.49 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 59506688 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.82 sec [bwa_aln_core] refine gapped alignments... 2.60 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 59768832 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.08 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 60030976 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.38 sec [bwa_aln_core] refine gapped alignments... 3.16 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 60293120 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.53 sec [bwa_aln_core] refine gapped alignments... 3.53 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 60555264 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.05 sec [bwa_aln_core] refine gapped alignments... 4.22 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 60817408 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.87 sec [bwa_aln_core] refine gapped alignments... 4.23 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 61079552 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.07 sec [bwa_aln_core] refine gapped alignments... 4.01 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 61341696 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.79 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 61603840 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.87 sec [bwa_aln_core] refine gapped alignments... 4.29 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 61865984 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.80 sec [bwa_aln_core] refine gapped alignments... 4.07 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 62128128 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.86 sec [bwa_aln_core] refine gapped alignments... 3.78 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 62390272 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.29 sec [bwa_aln_core] refine gapped alignments... 2.42 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 62652416 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.55 sec [bwa_aln_core] refine gapped alignments... 2.37 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 62914560 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.59 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 63176704 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.26 sec [bwa_aln_core] refine gapped alignments... 2.36 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 63438848 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.46 sec [bwa_aln_core] refine gapped alignments... 2.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 63700992 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.28 sec [bwa_aln_core] refine gapped alignments... 2.32 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 63963136 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.53 sec [bwa_aln_core] refine gapped alignments... 2.37 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 64225280 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.48 sec [bwa_aln_core] refine gapped alignments... 2.36 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 64487424 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.65 sec [bwa_aln_core] refine gapped alignments... 2.31 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 64749568 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.71 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 65011712 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.90 sec [bwa_aln_core] refine gapped alignments... 1.64 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 65273856 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.61 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 65536000 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.35 sec [bwa_aln_core] refine gapped alignments... 2.97 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 65798144 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.04 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 66060288 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.51 sec [bwa_aln_core] refine gapped alignments... 2.88 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 66322432 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.61 sec [bwa_aln_core] refine gapped alignments... 3.66 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 66584576 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.11 sec [bwa_aln_core] refine gapped alignments... 3.20 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 66846720 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.91 sec [bwa_aln_core] refine gapped alignments... 4.47 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 67108864 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.30 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 67371008 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.64 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 67633152 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.18 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 67895296 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.55 sec [bwa_aln_core] refine gapped alignments... 3.52 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 68157440 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.84 sec [bwa_aln_core] refine gapped alignments... 0.97 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 68419584 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.57 sec [bwa_aln_core] refine gapped alignments... 4.78 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 68681728 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.73 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 68943872 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.28 sec [bwa_aln_core] refine gapped alignments... 3.99 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 69206016 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.09 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 69468160 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.00 sec [bwa_aln_core] refine gapped alignments... 2.73 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 69730304 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.75 sec [bwa_aln_core] refine gapped alignments... 4.40 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 69992448 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.45 sec [bwa_aln_core] refine gapped alignments... 5.68 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 70254592 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.93 sec [bwa_aln_core] refine gapped alignments... 3.27 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 70516736 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.20 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 70778880 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.15 sec [bwa_aln_core] refine gapped alignments... 1.08 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 71041024 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.03 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 71303168 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.91 sec [bwa_aln_core] refine gapped alignments... 3.37 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 71565312 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.96 sec [bwa_aln_core] refine gapped alignments... 4.71 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 71827456 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.19 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 72089600 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.38 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 72351744 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.76 sec [bwa_aln_core] refine gapped alignments... 4.30 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 72613888 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.48 sec [bwa_aln_core] refine gapped alignments... 0.96 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 72876032 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.45 sec [bwa_aln_core] refine gapped alignments... 4.22 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 73138176 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.61 sec [bwa_aln_core] refine gapped alignments... 2.29 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 73400320 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.50 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 73662464 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.07 sec [bwa_aln_core] refine gapped alignments... 3.27 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 73924608 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.47 sec [bwa_aln_core] refine gapped alignments... 3.30 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 74186752 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.82 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 74448896 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.30 sec [bwa_aln_core] refine gapped alignments... 1.99 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 74711040 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.54 sec [bwa_aln_core] refine gapped alignments... 4.02 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 74973184 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.46 sec [bwa_aln_core] refine gapped alignments... 4.05 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 75235328 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.19 sec [bwa_aln_core] refine gapped alignments... 5.97 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 75497472 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.73 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 75759616 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.04 sec [bwa_aln_core] refine gapped alignments... 3.02 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 76021760 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.01 sec [bwa_aln_core] refine gapped alignments... 2.67 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 76283904 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.07 sec [bwa_aln_core] refine gapped alignments... 2.74 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 76546048 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.49 sec [bwa_aln_core] refine gapped alignments... 4.28 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 76808192 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.33 sec [bwa_aln_core] refine gapped alignments... 5.77 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 77070336 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.06 sec [bwa_aln_core] refine gapped alignments... 4.58 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 77332480 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.48 sec [bwa_aln_core] refine gapped alignments... 3.78 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 77594624 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.90 sec [bwa_aln_core] refine gapped alignments... 1.58 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 77856768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.31 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 78118912 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.47 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 78381056 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.72 sec [bwa_aln_core] refine gapped alignments... 2.92 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 78643200 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.67 sec [bwa_aln_core] refine gapped alignments... 6.02 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 78905344 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.77 sec [bwa_aln_core] refine gapped alignments... 2.97 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 79167488 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.58 sec [bwa_aln_core] refine gapped alignments... 2.91 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 79429632 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.28 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 79691776 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.65 sec [bwa_aln_core] refine gapped alignments... 1.86 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 79953920 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.15 sec [bwa_aln_core] refine gapped alignments... 3.88 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 80216064 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.30 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 80478208 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.74 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 80740352 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.36 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 81002496 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.34 sec [bwa_aln_core] refine gapped alignments... 3.11 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 81264640 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.31 sec [bwa_aln_core] refine gapped alignments... 3.95 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 81526784 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.30 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 81788928 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.92 sec [bwa_aln_core] refine gapped alignments... 6.11 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 82051072 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.41 sec [bwa_aln_core] refine gapped alignments... 5.77 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 82313216 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.91 sec [bwa_aln_core] refine gapped alignments... 4.20 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 82575360 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.36 sec [bwa_aln_core] refine gapped alignments... 1.27 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 82837504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.56 sec [bwa_aln_core] refine gapped alignments... 3.19 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 83099648 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.35 sec [bwa_aln_core] refine gapped alignments... 2.27 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 83361792 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.70 sec [bwa_aln_core] refine gapped alignments... 3.80 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 83623936 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.91 sec [bwa_aln_core] refine gapped alignments... 3.89 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 83886080 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.40 sec [bwa_aln_core] refine gapped alignments... 2.57 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 84148224 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.34 sec [bwa_aln_core] refine gapped alignments... 2.83 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 84410368 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.41 sec [bwa_aln_core] refine gapped alignments... 2.65 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 84672512 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.91 sec [bwa_aln_core] refine gapped alignments... 2.80 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 84934656 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.05 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 85196800 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.07 sec [bwa_aln_core] refine gapped alignments... 2.92 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 85458944 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.56 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 85721088 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.55 sec [bwa_aln_core] refine gapped alignments... 1.71 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 85983232 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.57 sec [bwa_aln_core] refine gapped alignments... 1.70 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 86245376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.15 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 86507520 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.21 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 86769664 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.81 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 87031808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.87 sec [bwa_aln_core] refine gapped alignments... 1.06 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 87293952 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.32 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 87556096 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.61 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 87818240 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.27 sec [bwa_aln_core] refine gapped alignments... 3.66 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 88080384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.27 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 88342528 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.13 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 88604672 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.47 sec [bwa_aln_core] refine gapped alignments... 2.68 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 88866816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.98 sec [bwa_aln_core] refine gapped alignments... 2.95 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 89128960 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.46 sec [bwa_aln_core] refine gapped alignments... 3.27 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 89391104 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.56 sec [bwa_aln_core] refine gapped alignments... 2.89 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 89653248 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.31 sec [bwa_aln_core] refine gapped alignments... 2.14 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 89915392 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.76 sec [bwa_aln_core] refine gapped alignments... 2.49 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 90177536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.72 sec [bwa_aln_core] refine gapped alignments... 2.74 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 90439680 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.37 sec [bwa_aln_core] refine gapped alignments... 2.89 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 90701824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.82 sec [bwa_aln_core] refine gapped alignments... 2.31 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 90963968 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.80 sec [bwa_aln_core] refine gapped alignments... 1.92 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 91226112 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.84 sec [bwa_aln_core] refine gapped alignments... 1.96 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 91488256 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.67 sec [bwa_aln_core] refine gapped alignments... 1.97 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 91750400 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.37 sec [bwa_aln_core] refine gapped alignments... 3.08 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 92012544 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.47 sec [bwa_aln_core] refine gapped alignments... 3.81 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 92274688 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.25 sec [bwa_aln_core] refine gapped alignments... 3.78 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 92536832 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.67 sec [bwa_aln_core] refine gapped alignments... 2.16 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 92798976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.07 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 93061120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.27 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 93323264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.60 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 93585408 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.59 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 93847552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.42 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 94109696 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.84 sec [bwa_aln_core] refine gapped alignments... 6.36 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 94371840 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.43 sec [bwa_aln_core] refine gapped alignments... 4.62 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 94633984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.44 sec [bwa_aln_core] refine gapped alignments... 4.26 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 94896128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.14 sec [bwa_aln_core] refine gapped alignments... 4.72 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 95158272 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.15 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 95420416 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.46 sec [bwa_aln_core] refine gapped alignments... 3.88 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 95682560 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.79 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 95944704 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.02 sec [bwa_aln_core] refine gapped alignments... 4.61 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 96206848 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.07 sec [bwa_aln_core] refine gapped alignments... 1.96 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 96468992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.70 sec [bwa_aln_core] refine gapped alignments... 2.98 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 96731136 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.38 sec [bwa_aln_core] refine gapped alignments... 1.86 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 96993280 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.22 sec [bwa_aln_core] refine gapped alignments... 6.17 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 97255424 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.36 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 97517568 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.56 sec [bwa_aln_core] refine gapped alignments... 5.43 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 97779712 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.13 sec [bwa_aln_core] refine gapped alignments... 2.27 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 98041856 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.37 sec [bwa_aln_core] refine gapped alignments... 2.06 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 98304000 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.80 sec [bwa_aln_core] refine gapped alignments... 3.18 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 98566144 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.41 sec [bwa_aln_core] refine gapped alignments... 2.98 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 98828288 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.97 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 99090432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.53 sec [bwa_aln_core] refine gapped alignments... 3.52 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 99352576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.69 sec [bwa_aln_core] refine gapped alignments... 1.47 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 99614720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.53 sec [bwa_aln_core] refine gapped alignments... 3.74 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 99876864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.06 sec [bwa_aln_core] refine gapped alignments... 3.24 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 100139008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.85 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 100401152 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.41 sec [bwa_aln_core] refine gapped alignments... 4.50 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 100663296 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.62 sec [bwa_aln_core] refine gapped alignments... 4.25 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 100925440 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.47 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 101187584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.15 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 101449728 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.41 sec [bwa_aln_core] refine gapped alignments... 1.27 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 101711872 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.67 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 101974016 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.41 sec [bwa_aln_core] refine gapped alignments... 2.92 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 102236160 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.13 sec [bwa_aln_core] refine gapped alignments... 2.11 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 102498304 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.71 sec [bwa_aln_core] refine gapped alignments... 2.29 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 102760448 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.63 sec [bwa_aln_core] refine gapped alignments... 3.63 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 103022592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.11 sec [bwa_aln_core] refine gapped alignments... 1.44 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 103284736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.58 sec [bwa_aln_core] refine gapped alignments... 3.29 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 103546880 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.24 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 103809024 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.77 sec [bwa_aln_core] refine gapped alignments... 0.71 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 104071168 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.87 sec [bwa_aln_core] refine gapped alignments... 1.54 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 104333312 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.21 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 104595456 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.65 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 104857600 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.16 sec [bwa_aln_core] refine gapped alignments... 2.83 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 105119744 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.11 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 105381888 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.39 sec [bwa_aln_core] refine gapped alignments... 3.72 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 105644032 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.15 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 105906176 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.06 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 106168320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.62 sec [bwa_aln_core] refine gapped alignments... 4.18 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 106430464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.83 sec [bwa_aln_core] refine gapped alignments... 3.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 106692608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.33 sec [bwa_aln_core] refine gapped alignments... 2.21 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 106954752 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.41 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 107216896 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.36 sec [bwa_aln_core] refine gapped alignments... 2.97 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 107479040 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.03 sec [bwa_aln_core] refine gapped alignments... 0.74 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 107741184 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.97 sec [bwa_aln_core] refine gapped alignments... 5.62 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 108003328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.39 sec [bwa_aln_core] refine gapped alignments... 2.87 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 108265472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.98 sec [bwa_aln_core] refine gapped alignments... 2.05 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 108527616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.39 sec [bwa_aln_core] refine gapped alignments... 2.64 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 108789760 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.28 sec [bwa_aln_core] refine gapped alignments... 2.34 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 109051904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.93 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 109314048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.91 sec [bwa_aln_core] refine gapped alignments... 4.84 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 109576192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.04 sec [bwa_aln_core] refine gapped alignments... 3.62 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 109838336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.59 sec [bwa_aln_core] refine gapped alignments... 3.63 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 110100480 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.82 sec [bwa_aln_core] refine gapped alignments... 4.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 110362624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.76 sec [bwa_aln_core] refine gapped alignments... 4.69 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 110624768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.04 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 110886912 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.55 sec [bwa_aln_core] refine gapped alignments... 4.25 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 111149056 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.44 sec [bwa_aln_core] refine gapped alignments... 4.32 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 111411200 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.63 sec [bwa_aln_core] refine gapped alignments... 3.65 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 111673344 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.35 sec [bwa_aln_core] refine gapped alignments... 4.01 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 111935488 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.78 sec [bwa_aln_core] refine gapped alignments... 4.27 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 112197632 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.86 sec [bwa_aln_core] refine gapped alignments... 3.49 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 112459776 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.59 sec [bwa_aln_core] refine gapped alignments... 3.08 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 112721920 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.56 sec [bwa_aln_core] refine gapped alignments... 3.03 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 112984064 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.33 sec [bwa_aln_core] refine gapped alignments... 2.79 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 113246208 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.80 sec [bwa_aln_core] refine gapped alignments... 2.90 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 113508352 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.50 sec [bwa_aln_core] refine gapped alignments... 2.72 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 113770496 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.22 sec [bwa_aln_core] refine gapped alignments... 2.87 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 114023882 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/ZF6/out/align/rep1/ZF6_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF6_allReps.fastq.gz [main] Real time: 13896.984 sec; CPU: 13724.556 sec | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/rep1/ZF6_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_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/ZF6/out/align/rep1/ZF6_allReps.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_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-------------------- 34061 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# 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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 48338 (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 22:49:14 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_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 [Wed Sep 28 22:49:14 PDT 2016] Executing as imk1@nandi on Linux 3.16.0-67-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory) INFO 2016-09-28 22:49:14 MarkDuplicates Start of doWork freeMemory: 255389968; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-28 22:49:14 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-28 22:49:14 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. WARNING 2016-09-28 22:49:17 AbstractDuplicateFindingAlgorithm Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836482.4370814'. 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 2016-09-28 22:49:31 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:42,985,407 INFO 2016-09-28 22:49:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:49:39 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 7s. Last read position: chr1:77,699,637 INFO 2016-09-28 22:49:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:49:53 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 14s. Last read position: chr1:112,701,622 INFO 2016-09-28 22:49:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:49:58 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 5s. Last read position: chr1:143,554,762 INFO 2016-09-28 22:49:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 15s. Last read position: chr1:171,111,325 INFO 2016-09-28 22:50:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:17 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr1:194,789,481 INFO 2016-09-28 22:50:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:21 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr2:29,896,159 INFO 2016-09-28 22:50:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:27 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 5s. Last read position: chr2:57,191,799 INFO 2016-09-28 22:50:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:30 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr2:88,458,099 INFO 2016-09-28 22:50:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:34 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 4s. Last read position: chr2:119,294,976 INFO 2016-09-28 22:50:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:40 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 6s. Last read position: chr2:145,805,110 INFO 2016-09-28 22:50:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr2:166,995,743 INFO 2016-09-28 22:50:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 7s. Last read position: chr3:22,651,530 INFO 2016-09-28 22:50:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:55 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr3:63,269,930 INFO 2016-09-28 22:50:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:50:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 4s. Last read position: chr3:94,838,195 INFO 2016-09-28 22:50:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:12 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 12s. Last read position: chr3:121,235,980 INFO 2016-09-28 22:51:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:15 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chr3:149,880,161 INFO 2016-09-28 22:51:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:19 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 4s. Last read position: chr4:34,473,995 INFO 2016-09-28 22:51:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:20 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr4:64,324,470 INFO 2016-09-28 22:51:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:22 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr4:106,935,404 INFO 2016-09-28 22:51:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:26 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: chr4:130,087,977 INFO 2016-09-28 22:51:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:28 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr4:149,197,628 INFO 2016-09-28 22:51:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:31 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr5:28,470,858 INFO 2016-09-28 22:51:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:34 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr5:63,001,374 INFO 2016-09-28 22:51:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:41 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 7s. Last read position: chr5:99,514,185 INFO 2016-09-28 22:51:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:44 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr5:121,446,014 INFO 2016-09-28 22:51:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:48 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 4s. Last read position: chr5:140,914,431 INFO 2016-09-28 22:51:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:52 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: chr6:25,664,699 INFO 2016-09-28 22:51:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:51:59 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 6s. Last read position: chr6:54,645,544 INFO 2016-09-28 22:51:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:01 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr6:89,358,135 INFO 2016-09-28 22:52:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:14 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 12s. Last read position: chr6:119,459,297 INFO 2016-09-28 22:52:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:17 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr6:145,931,138 INFO 2016-09-28 22:52:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:21 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 4s. Last read position: chr7:31,000,706 INFO 2016-09-28 22:52:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:28 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 7s. Last read position: chr7:69,159,912 INFO 2016-09-28 22:52:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:31 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr7:99,763,790 INFO 2016-09-28 22:52:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:33 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr7:125,618,475 INFO 2016-09-28 22:52:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:36 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr8:7,567,725 INFO 2016-09-28 22:52:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:39 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr8:45,763,237 INFO 2016-09-28 22:52:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:43 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 4s. Last read position: chr8:80,975,855 INFO 2016-09-28 22:52:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:46 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr8:107,862,105 INFO 2016-09-28 22:52:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:50 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 3s. Last read position: chr8:128,898,154 INFO 2016-09-28 22:52:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:54 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 4s. Last read position: chr9:40,906,857 INFO 2016-09-28 22:52:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:52:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 3s. Last read position: chr9:62,980,455 INFO 2016-09-28 22:52:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:04 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 6s. Last read position: chr9:89,964,940 INFO 2016-09-28 22:53:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:07 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr9:115,770,949 INFO 2016-09-28 22:53:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:20 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 13s. Last read position: chr10:22,668,120 INFO 2016-09-28 22:53:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:23 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr10:59,615,366 INFO 2016-09-28 22:53:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:26 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 3s. Last read position: chr10:81,127,958 INFO 2016-09-28 22:53:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:31 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 4s. Last read position: chr10:108,912,871 INFO 2016-09-28 22:53:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:35 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 4s. Last read position: chr11:5,961,965 INFO 2016-09-28 22:53:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:41 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 5s. Last read position: chr11:41,317,885 INFO 2016-09-28 22:53:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:44 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr11:63,627,286 INFO 2016-09-28 22:53:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:46 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr11:82,915,404 INFO 2016-09-28 22:53:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:49 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr11:101,181,034 INFO 2016-09-28 22:53:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:51 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr11:118,120,484 INFO 2016-09-28 22:53:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:56 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 4s. Last read position: chr12:34,847,877 INFO 2016-09-28 22:53:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:53:59 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr12:75,724,109 INFO 2016-09-28 22:53:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:02 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 3s. Last read position: chr12:102,088,430 INFO 2016-09-28 22:54:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:07 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 4s. Last read position: chr13:17,193,469 INFO 2016-09-28 22:54:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:11 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 4s. Last read position: chr13:45,266,587 INFO 2016-09-28 22:54:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:24 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 13s. Last read position: chr13:74,458,157 INFO 2016-09-28 22:54:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:27 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr13:107,735,204 INFO 2016-09-28 22:54:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:31 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 4s. Last read position: chr14:28,644,523 INFO 2016-09-28 22:54:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:34 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr14:62,150,266 INFO 2016-09-28 22:54:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:36 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr14:94,882,921 INFO 2016-09-28 22:54:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:39 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr15:11,698,703 INFO 2016-09-28 22:54:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:42 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr15:58,578,352 INFO 2016-09-28 22:54:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:45 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr15:81,912,796 INFO 2016-09-28 22:54:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:49 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 4s. Last read position: chr15:103,068,254 INFO 2016-09-28 22:54:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:52 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr16:29,874,326 INFO 2016-09-28 22:54:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:55 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 3s. Last read position: chr16:57,990,053 INFO 2016-09-28 22:54:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:54:59 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 3s. Last read position: chr16:95,305,848 INFO 2016-09-28 22:54:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:03 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 3s. Last read position: chr17:28,471,558 INFO 2016-09-28 22:55:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:13 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 10s. Last read position: chr17:46,991,019 INFO 2016-09-28 22:55:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:16 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr17:77,708,480 INFO 2016-09-28 22:55:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:28 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 11s. Last read position: chr18:20,050,511 INFO 2016-09-28 22:55:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:31 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 3s. Last read position: chr18:54,900,899 INFO 2016-09-28 22:55:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:35 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 4s. Last read position: chr18:81,687,026 INFO 2016-09-28 22:55:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:38 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 3s. Last read position: chr19:23,606,168 INFO 2016-09-28 22:55:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:43 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 4s. Last read position: chr19:47,588,775 INFO 2016-09-28 22:55:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:47 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 4s. Last read position: chrX:63,109,680 INFO 2016-09-28 22:55:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:51 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 4s. Last read position: chrX:159,941,429 INFO 2016-09-28 22:55:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 22:55:52 MarkDuplicates Read 82267088 records. 0 pairs never matched. INFO 2016-09-28 22:55:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 2669035472; totalMemory: 2755854336; maxMemory: 3817799680 INFO 2016-09-28 22:55:56 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-28 22:55:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-28 22:55:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-28 22:56:28 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-28 22:56:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 2098299712; totalMemory: 3078356992; maxMemory: 3817799680 INFO 2016-09-28 22:56:31 MarkDuplicates Marking 48158753 records as duplicates. INFO 2016-09-28 22:56:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-28 22:58:18 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:46s. Time for last 10,000,000: 106s. Last read position: chr2:119,294,976 INFO 2016-09-28 23:00:06 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 108s. Last read position: chr4:106,935,404 INFO 2016-09-28 23:02:00 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:05:29s. Time for last 10,000,000: 114s. Last read position: chr6:89,358,135 INFO 2016-09-28 23:04:02 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:07:31s. Time for last 10,000,000: 121s. Last read position: chr8:107,862,105 INFO 2016-09-28 23:06:02 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:09:31s. Time for last 10,000,000: 120s. Last read position: chr11:5,961,965 INFO 2016-09-28 23:08:00 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:11:28s. Time for last 10,000,000: 117s. Last read position: chr13:45,266,587 INFO 2016-09-28 23:09:53 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:13:22s. Time for last 10,000,000: 113s. Last read position: chr16:29,874,326 INFO 2016-09-28 23:11:54 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:15:22s. Time for last 10,000,000: 120s. Last read position: chr19:47,588,775 INFO 2016-09-28 23:12:22 MarkDuplicates Before output close freeMemory: 3146722464; totalMemory: 3176464384; maxMemory: 3817799680 INFO 2016-09-28 23:12:22 MarkDuplicates After output close freeMemory: 3146721624; totalMemory: 3176464384; maxMemory: 3817799680 [Wed Sep 28 23:12:22 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 23.14 minutes. Runtime.totalMemory()=3176464384 | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/rep1/ZF6_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_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/ZF6/out/qc/rep1/ZF6_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-------------------- 35236 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# 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/ZF6/out/align/rep1/ZF6_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 8902 (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 $$
# SYS command. line 46
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.15M.tagAlign.gz
# SYS command. line 49
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 8994 (process ID) old priority 0, new priority 10 Waiting for 27 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 249
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 252
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz | wc -l )
# SYS command. line 253
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 257
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.
# SYS command. line 260
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.pr1.tagAlign.gz
# SYS command. line 261
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.00
# SYS command. line 262
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr2/ZF6_allReps.nodup.pr2.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/pseudo_reps/rep1/pr1/ZF6_allReps.nodup.01
# SYS command. line 265
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 8995 (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/ZF6/out/align/rep1/ZF6_allReps.nodup.15M.tagAlign.gz -p=4 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_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--------------------
4017 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_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/ZF6/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/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/qc/rep1/ZF6_allReps.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.15M.tagAlign.gz
opened /tmp/9758.1.q/Rtmp2sFu2e/ZF6_allReps.nodup.15M.tagAlignff367d195ae
done. read 15000000 fragments
ChIP data read length 36
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1994509
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.223558524503926,0.22355620860897,0.212329962043561
Top 3 estimates for fragment length 160,170,305
Window half size 575
Phantom peak location 40
Phantom peak Correlation 0.2146942
Normalized Strand cross-correlation coefficient (NSC) 1.12087
Relative Strand Cross correlation Coefficient (RSC) 1.581519
Phantom Peak Quality Tag 2
null device
1
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
| ||||||||||||||||||||||||||||||||||||||||
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|
|
# 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/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_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/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
--------------------Stdout--------------------
9365 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 160
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_allReps.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/peak/spp/rep1/ZF6_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/ZF6/out/align/rep1/ZF6_allReps.nodup.tagAlign.gz
opened /tmp/9761.1.q/RtmpIPRG2M/ZF6_allReps.nodup.tagAlign24d74cab601c
done. read 34108335 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
opened /tmp/9761.1.q/RtmpIPRG2M/mousePrimaryBCellInput.nodup.tagAlign24d7f984170
done. read 15331612 fragments
Control data read length 36
Calculating peak characteristics
Minimum cross-correlation value 0.3537288
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.396503797071789
Top 3 estimates for fragment length 160
Window half size 575
Phantom peak location 55
Phantom peak Correlation 0.3813192
Normalized Strand cross-correlation coefficient (NSC) 1.120926
Relative Strand Cross correlation Coefficient (RSC) 1.550359
Phantom Peak Quality Tag 2
null device
1
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.5091676 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 1.96399
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
|
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, ZF6, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF6/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF6_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DISPLAY | localhost:19.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/keras |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_eHVWt0 |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5 |
| string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF6 |
| string | PYTHONPATH | /software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SGE_CELL | default |
| string | SGE_ROOT | /var/lib/gridengine |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 58475 22 |
| string | SSH_CONNECTION | 171.65.77.8 58475 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/38 |
| string | STY | 4607.ZF6.BDS |
| string | system | sge |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
| int | timeout | -1 |
| string | USER | imk1 |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1048 |
| string | XDG_SESSION_ID | 418 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |