| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161101_222026_419 |
| Start time | 2016-11-01 22:20:26 |
| Run time | 09:15:13.582 |
| Tasks executed | 15 |
| Tasks failed | 1 |
| Tasks failed names | xcor rep1 |
| Arguments* | [-title, SRR836497, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_41 | thread_Root | chipseq.bds.20161101_222026_419_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161101_222026_419_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_12 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_17 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_18 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24 |
| thread_42 | thread_Root | chipseq.bds.20161101_222026_419_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20161101_222026_419_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_13 chipseq.bds.20161101_222026_419_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20161101_222026_419_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15 chipseq.bds.20161101_222026_419_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16 chipseq.bds.20161101_222026_419_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_19 |
| 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 3 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.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-------------------- 53932 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.19 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.41 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.69 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.25 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.72 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.35 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.64 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.35 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.36 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.92 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.95 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.85 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.61 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.30 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.24 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.42 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.34 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.11 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.11 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.92 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.36 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.32 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.48 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.45 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.31 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.76 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.29 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.77 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.51 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.50 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.51 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.19 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.64 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.39 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.62 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.76 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.85 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.72 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.06 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.67 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.54 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.79 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.19 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.79 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.36 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.30 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.83 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.82 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.89 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.57 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.03 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.21 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.92 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.75 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.63 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.66 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.37 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.48 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.64 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.45 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.02 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.88 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.99 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.44 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.26 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.46 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.22 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.54 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.05 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.14 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.68 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.26 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.09 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.33 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.35 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.07 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.22 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.92 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.05 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.29 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.41 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.47 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.07 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.50 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.58 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.29 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.60 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.83 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.11 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.93 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.74 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.12 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.15 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.21 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.99 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.88 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.64 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.97 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.47 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.24 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.60 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.20 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.76 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.37 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.21 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.84 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.45 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.11 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 0.01 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 50069536 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 3 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz [main] Real time: 4359.443 sec; CPU: 12473.424 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 2 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 25826 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.90 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.85 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.30 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.84 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.47 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.22 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.53 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.36 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.87 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% 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] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.92 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.36 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.61 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.53 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.93 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.35 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.85 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.17 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.87 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% 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] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% 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] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.36 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.37 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% 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] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.65 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% 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] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.65 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.22 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 7.02 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 32022635 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz [main] Real time: 2649.928 sec; CPU: 5191.712 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/SRR836497/out/align/rep1/SRR836497.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.bam
# SYS command. line 149
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.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-------------------- 6827 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.48 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.21 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.17 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.99 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.89 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.08 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.04 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.57 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.19 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.73 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.43 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.97 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.90 sec [bwa_aln_core] refine gapped alignments... 2.85 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.12 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.27 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.90 sec [bwa_aln_core] refine gapped alignments... 2.00 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.12 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.18 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.87 sec [bwa_aln_core] refine gapped alignments... 0.68 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.47 sec [bwa_aln_core] refine gapped alignments... 3.17 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.71 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.64 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.75 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.62 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.41 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.07 sec [bwa_aln_core] refine gapped alignments... 1.68 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.07 sec [bwa_aln_core] refine gapped alignments... 1.90 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.90 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.22 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.44 sec [bwa_aln_core] refine gapped alignments... 3.04 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.22 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.75 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.31 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.23 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.98 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.91 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.84 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.78 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.14 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.68 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.96 sec [bwa_aln_core] refine gapped alignments... 0.95 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.20 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.87 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.64 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.95 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.41 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.51 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.06 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.33 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.01 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.39 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.53 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.62 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.43 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.71 sec [bwa_aln_core] refine gapped alignments... 1.70 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.24 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.15 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.52 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.51 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.00 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.41 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.72 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.54 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.43 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.26 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.48 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.78 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.14 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.18 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.40 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.93 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.90 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.06 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.96 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.65 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.01 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.35 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.68 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.07 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.11 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.19 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.29 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.10 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.48 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.46 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.75 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.05 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.01 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.09 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.54 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.00 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.94 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.59 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.64 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.51 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.14 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.07 sec [bwa_aln_core] refine gapped alignments... 1.90 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.01 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.19 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.43 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.54 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.52 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.94 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.37 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.40 sec [bwa_aln_core] refine gapped alignments... 0.92 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.74 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.45 sec [bwa_aln_core] refine gapped alignments... 2.20 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.93 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.39 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.25 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.53 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.89 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.43 sec [bwa_aln_core] refine gapped alignments... 0.89 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.44 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.14 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.48 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.01 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.81 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.90 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.99 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.10 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.66 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.92 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.84 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.29 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.13 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.24 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.31 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.78 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.93 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.05 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.04 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.67 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.76 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.90 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.93 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.26 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.64 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.82 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.59 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.05 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.36 sec [bwa_aln_core] refine gapped alignments... 0.82 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.80 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.79 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.35 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.40 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.95 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.09 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.66 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.96 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.06 sec [bwa_aln_core] refine gapped alignments... 1.25 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.48 sec [bwa_aln_core] refine gapped alignments... 1.01 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.39 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.99 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.28 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.91 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.26 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.48 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.76 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.28 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.70 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.04 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.04 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.06 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.78 sec [bwa_aln_core] refine gapped alignments... 1.67 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.65 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.79 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.58 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.70 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.24 sec [bwa_aln_core] refine gapped alignments... 1.03 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.56 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.86 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.28 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.04 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.53 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.03 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.62 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.88 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.36 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.79 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.48 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.27 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.48 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.14 sec [bwa_aln_core] refine gapped alignments... 0.99 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.44 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.98 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.86 sec [bwa_aln_core] refine gapped alignments... 0.28 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 50069536 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/SRR836497/out/align/rep1/SRR836497.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz [main] Real time: 2121.931 sec; CPU: 2027.284 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/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
# SYS command. line 149
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 25030 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.19 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.60 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.28 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.40 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.48 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.74 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.97 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.67 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.61 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.66 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.55 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.58 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.74 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.34 sec [bwa_aln_core] refine gapped alignments... 0.73 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.62 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.60 sec [bwa_aln_core] refine gapped alignments... 0.62 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.44 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.74 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.63 sec [bwa_aln_core] refine gapped alignments... 0.69 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.69 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.63 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.53 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.26 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.46 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.36 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.46 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.40 sec [bwa_aln_core] refine gapped alignments... 0.63 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.52 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.85 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.35 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.84 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.50 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.55 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.57 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.80 sec [bwa_aln_core] refine gapped alignments... 0.75 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.87 sec [bwa_aln_core] refine gapped alignments... 0.61 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.52 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.55 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.91 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.92 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.60 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.78 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.22 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.86 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.29 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.68 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.85 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.43 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.31 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.30 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.57 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.46 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.36 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.78 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.70 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.57 sec [bwa_aln_core] refine gapped alignments... 0.72 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.34 sec [bwa_aln_core] refine gapped alignments... 3.87 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.20 sec [bwa_aln_core] refine gapped alignments... 4.11 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.15 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.97 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.45 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.40 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.49 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.53 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.45 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.42 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.19 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.50 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.25 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.57 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.21 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.32 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.26 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.26 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.75 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.20 sec [bwa_aln_core] refine gapped alignments... 0.70 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.72 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.80 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.54 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.79 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.21 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.30 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.78 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.20 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.77 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.24 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.76 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.91 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.70 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.84 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.83 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.43 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.37 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.39 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.31 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.63 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.73 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.74 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.83 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.64 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.80 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.75 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.52 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.71 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.52 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.55 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.10 sec [bwa_aln_core] 32022635 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz [main] Real time: 987.535 sec; CPU: 789.884 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 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 47424 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 1012 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Nov 02 06:10:26 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Nov 02 06:10:26 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-02 06:10:26 MarkDuplicates Start of doWork freeMemory: 254882928; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-11-02 06:10:26 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-02 06:10:26 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-11-02 06:10:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: chr1:169,651,309 INFO 2016-11-02 06:10:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:10:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 4s. Last read position: chr2:120,600,340 INFO 2016-11-02 06:10:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:10:42 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 4s. Last read position: chr3:96,659,413 INFO 2016-11-02 06:10:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:10:47 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 4s. Last read position: chr4:108,195,091 INFO 2016-11-02 06:10:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:10:52 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 4s. Last read position: chr5:103,594,339 INFO 2016-11-02 06:10:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:10:57 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 4s. Last read position: chr6:98,592,333 INFO 2016-11-02 06:10:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:00 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr7:114,109,505 INFO 2016-11-02 06:11:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:06 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: chr8:121,515,352 INFO 2016-11-02 06:11:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:13 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 6s. Last read position: chr10:14,536,964 INFO 2016-11-02 06:11:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:16 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr11:32,924,585 INFO 2016-11-02 06:11:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:21 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 5s. Last read position: chr12:41,050,039 INFO 2016-11-02 06:11:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:26 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 4s. Last read position: chr13:80,878,598 INFO 2016-11-02 06:11:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:30 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 4s. Last read position: chr15:12,027,335 INFO 2016-11-02 06:11:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:34 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr16:56,024,589 INFO 2016-11-02 06:11:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 21s. Last read position: chr18:10,030,498 INFO 2016-11-02 06:11:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:01 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 5s. Last read position: chrX:36,565,109 INFO 2016-11-02 06:12:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:03 MarkDuplicates Read 16572675 records. 0 pairs never matched. INFO 2016-11-02 06:12:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 2050317344; totalMemory: 2125987840; maxMemory: 3817865216 INFO 2016-11-02 06:12:04 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk. INFO 2016-11-02 06:12:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-02 06:12:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-02 06:12:15 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-02 06:12:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 1446175128; totalMemory: 2418016256; maxMemory: 3817865216 INFO 2016-11-02 06:12:15 MarkDuplicates Marking 13188493 records as duplicates. INFO 2016-11-02 06:12:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-02 06:14:24 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:08s. Time for last 10,000,000: 128s. Last read position: chr11:32,924,585 INFO 2016-11-02 06:15:43 MarkDuplicates Before output close freeMemory: 2179721744; totalMemory: 2199388160; maxMemory: 3817865216 INFO 2016-11-02 06:15:44 MarkDuplicates After output close freeMemory: 2208032240; totalMemory: 2227699712; maxMemory: 3817865216 [Wed Nov 02 06:15:44 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.30 minutes. Runtime.totalMemory()=2227699712 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 153
sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 155
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 9206 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.bam | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 8099 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836497/out/align/rep1/SRR836497.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.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-------------------- 5980 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Nov 02 07:12:27 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Nov 02 07:12:27 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-02 07:12:27 MarkDuplicates Start of doWork freeMemory: 254883448; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-11-02 07:12:27 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-02 07:12:27 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. WARNING 2016-11-02 07:12:27 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836497.1787573'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-11-02 07:12:34 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:87,660,987 INFO 2016-11-02 07:12:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:12:39 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 4s. Last read position: chr1:165,837,574 INFO 2016-11-02 07:12:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:12:44 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 4s. Last read position: chr2:39,721,425 INFO 2016-11-02 07:12:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:12:49 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 4s. Last read position: chr2:119,091,683 INFO 2016-11-02 07:12:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:12:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 4s. Last read position: chr3:9,856,189 INFO 2016-11-02 07:12:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:12:58 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 4s. Last read position: chr3:95,542,963 INFO 2016-11-02 07:12:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:02 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 4s. Last read position: chr4:19,122,135 INFO 2016-11-02 07:13:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:09 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 6s. Last read position: chr4:107,363,700 INFO 2016-11-02 07:13:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:16 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 6s. Last read position: chr5:21,391,343 INFO 2016-11-02 07:13:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:20 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 4s. Last read position: chr5:103,727,702 INFO 2016-11-02 07:13:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:24 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 4s. Last read position: chr6:20,948,471 INFO 2016-11-02 07:13:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:28 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 4s. Last read position: chr6:99,600,414 INFO 2016-11-02 07:13:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:32 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr7:34,393,030 INFO 2016-11-02 07:13:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:36 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr7:113,846,894 INFO 2016-11-02 07:13:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:13:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 22s. Last read position: chr8:47,988,748 INFO 2016-11-02 07:13:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:03 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 4s. Last read position: chr8:122,277,696 INFO 2016-11-02 07:14:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:07 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 4s. Last read position: chr9:66,938,978 INFO 2016-11-02 07:14:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:11 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 4s. Last read position: chr10:18,503,569 INFO 2016-11-02 07:14:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:16 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 4s. Last read position: chr10:90,344,374 INFO 2016-11-02 07:14:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:21 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 4s. Last read position: chr11:38,761,594 INFO 2016-11-02 07:14:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:26 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 5s. Last read position: chr11:97,505,698 INFO 2016-11-02 07:14:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:32 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 6s. Last read position: chr12:50,053,100 INFO 2016-11-02 07:14:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:36 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 4s. Last read position: chr13:9,775,221 INFO 2016-11-02 07:14:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:40 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 4s. Last read position: chr13:91,211,128 INFO 2016-11-02 07:14:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:45 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 4s. Last read position: chr14:59,645,385 INFO 2016-11-02 07:14:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:50 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 4s. Last read position: chr15:22,064,865 INFO 2016-11-02 07:14:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:54 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 4s. Last read position: chr15:97,177,649 INFO 2016-11-02 07:14:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:14:58 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 4s. Last read position: chr16:65,916,223 INFO 2016-11-02 07:14:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:05 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 6s. Last read position: chr17:43,113,972 INFO 2016-11-02 07:15:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:16 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 10s. Last read position: chr18:32,113,969 INFO 2016-11-02 07:15:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:21 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 4s. Last read position: chr19:16,740,481 INFO 2016-11-02 07:15:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:26 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 4s. Last read position: chrX:54,077,775 INFO 2016-11-02 07:15:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:30 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 4s. Last read position: chrX:167,497,977 INFO 2016-11-02 07:15:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:15:30 MarkDuplicates Read 33137112 records. 0 pairs never matched. INFO 2016-11-02 07:15:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 2065269344; totalMemory: 2141716480; maxMemory: 3817865216 INFO 2016-11-02 07:15:32 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk. INFO 2016-11-02 07:15:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-02 07:15:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-02 07:15:45 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-02 07:15:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 1461914944; totalMemory: 2433744896; maxMemory: 3817865216 INFO 2016-11-02 07:15:46 MarkDuplicates Marking 9126435 records as duplicates. INFO 2016-11-02 07:15:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-02 07:17:52 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:05s. Time for last 10,000,000: 125s. Last read position: chr5:103,727,702 INFO 2016-11-02 07:19:52 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:04:05s. Time for last 10,000,000: 120s. Last read position: chr11:38,761,594 INFO 2016-11-02 07:21:49 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:06:02s. Time for last 10,000,000: 116s. Last read position: chr18:32,113,969 INFO 2016-11-02 07:22:25 MarkDuplicates Before output close freeMemory: 2244597568; totalMemory: 2264924160; maxMemory: 3817865216 INFO 2016-11-02 07:22:26 MarkDuplicates After output close freeMemory: 2242499360; totalMemory: 2262827008; maxMemory: 3817865216 [Wed Nov 02 07:22:26 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 9.99 minutes. Runtime.totalMemory()=2262827008 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 7285 (process ID) old priority 0, new priority 10 Waiting for 51 seconds. | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836497/out/align/rep1/SRR836497.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.bam
# SYS command. line 153
sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.bam
# SYS command. line 155
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.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/SRR836497/out/qc/rep1/SRR836497.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-------------------- 11059 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836497/out/align/rep1/SRR836497.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 39570 (process ID) old priority 0, new priority 10 Waiting for 4 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# 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 $$
# SYS command. line 46
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.15M.tagAlign.gz
# SYS command. line 49
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 12846 (process ID) old priority 0, new priority 10 Waiting for 31 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 249
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 252
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz | wc -l )
# SYS command. line 253
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 257
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.
# SYS command. line 260
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.pr1.tagAlign.gz
# SYS command. line 261
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.00
# SYS command. line 262
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr2/SRR836497.nodup.pr2.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/pseudo_reps/rep1/pr1/SRR836497.nodup.01
# SYS command. line 265
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 10869 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# 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 ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/align/rep1/SRR836497.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out/qc/rep1/SRR836497.nodup.15M.cc.qc
# SYS command. line 222
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
41550 (process ID) old priority 0, new priority 10
--------------------Post mortem info--------------------
==============================================================
job_number: 3292
submission_time: Wed Nov 2 07:35:32 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/chipseq.bds.20161101_222026_419_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 51178 22,USER=imk1,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5:/users/imk1/perl5:/users/imk1/perl5,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/18,LOGNAME=imk1,_=/usr/bin/bds,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect,PERL5LIB=/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5,DISPLAY=localhost:12.0,SGE_CELL=default,STY=37678.SRR836497.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_rUZelg,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 51178 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
parallel environment: shm range: 3
scheduling info: queue instance "q@mitra" dropped because it is temporarily not available
queue instance "amd.q@mitra" dropped because it is temporarily not available
queue instance "q@wotan" dropped because it is full
queue instance "amd.q@surya" dropped because it is full
queue instance "amd.q@kadru" dropped because it is full
queue instance "amd.q@kali" dropped because it is full
queue instance "amd.q@nandi" dropped because it is full
queue instance "amd.q@wotan" dropped because it is full
|
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, SRR836497, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836497/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836497.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DISPLAY | localhost:12.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_rUZelg |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5:/users/imk1/perl5:/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/SRR836497 |
| 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/SRR836497 |
| string | PYTHONPATH | /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 51178 22 |
| string | SSH_CONNECTION | 171.65.77.8 51178 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/18 |
| string | STY | 37678.SRR836497.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 |