| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161101_222026_772 |
| Start time | 2016-11-01 22:20:26 |
| Run time | 09:17:28.532 |
| Tasks executed | 15 |
| Tasks failed | 1 |
| Tasks failed names | xcor rep1 |
| Arguments* | [-title, SRR836496, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836496.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_772_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161101_222026_772_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_12 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_17 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_18 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20161101_222026_772_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24 |
| thread_42 | thread_Root | chipseq.bds.20161101_222026_772_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20161101_222026_772_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_13 chipseq.bds.20161101_222026_772_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20161101_222026_772_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15 chipseq.bds.20161101_222026_772_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16 chipseq.bds.20161101_222026_772_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/SRR836496.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.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-------------------- 37365 (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] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.55 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.8% 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] 5505024 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.9% 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] 6029312 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.22 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.34 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.72 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.87 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.8% 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] 15204352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.75 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.00 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.12 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.12 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.12 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.92 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.87 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.21 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.83 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.50 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.91 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.83 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.33 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.40 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.67 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.20 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.67 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.72 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.98 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.30 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.39 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.89 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.04 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.51 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.75 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.44 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 104.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 101.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 110.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 107.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 106.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 106.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 108.12 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.54 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.36 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.44 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.13 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.61 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.35 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.76 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... 97.26 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 49419522 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/SRR836496.fastq.gz [main] Real time: 5040.943 sec; CPU: 14494.724 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/SRR836496/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-------------------- 25665 (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... 48.36 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... 46.21 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... 46.51 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... 47.00 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... 46.52 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... 46.55 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... 46.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.66 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... 45.97 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... 46.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.50 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.61 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... 53.33 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... 50.94 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... 48.76 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... 45.16 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... 45.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.41 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.54 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... 49.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.46 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.02 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... 46.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.46 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... 44.90 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... 44.87 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... 44.53 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... 46.14 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... 53.15 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... 60.75 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... 60.63 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... 56.45 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.47 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... 45.57 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... 44.11 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... 49.06 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... 47.67 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... 48.82 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... 45.31 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... 45.93 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... 44.75 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.76 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... 44.76 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.01 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... 45.81 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... 45.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.23 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... 48.05 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... 50.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.11 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... 50.68 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.34 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... 46.07 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... 46.56 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... 44.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.95 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... 44.00 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... 45.89 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... 46.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.86 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... 45.85 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... 46.03 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... 45.36 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... 44.20 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... 44.83 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... 44.80 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... 45.46 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... 48.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.34 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... 53.55 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... 50.85 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... 48.26 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... 44.81 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... 44.03 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... 44.45 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... 44.51 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... 44.35 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... 46.59 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... 45.29 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... 45.34 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... 45.27 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... 44.38 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... 44.88 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... 46.80 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... 45.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.95 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... 47.65 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.64 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... 57.55 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... 57.56 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.76 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... 51.14 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... 48.66 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... 46.21 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... 44.77 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... 43.83 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... 44.69 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... 46.41 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... 45.09 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... 44.82 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... 44.74 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... 44.42 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... 45.42 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.05 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... 44.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.94 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... 43.66 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.97 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... 50.47 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... 51.23 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... 47.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.22 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... 45.02 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... 45.95 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... 46.68 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... 47.19 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... 47.90 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... 7.75 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: 2984.893 sec; CPU: 5858.120 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/SRR836496/out/align/rep1/SRR836496.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836496.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.bam
# SYS command. line 149
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.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-------------------- 8079 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.38 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.08 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.73 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.36 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.95 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.11 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.34 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.32 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.52 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.16 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.65 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.77 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.67 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.79 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.33 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.83 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.56 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.9% 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... 0.38 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.73 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.34 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.55 sec [bwa_aln_core] refine gapped alignments... 2.30 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.47 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.73 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.62 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.86 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.78 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.48 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.55 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.01 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.24 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.68 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.26 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.38 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.76 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.79 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.91 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.60 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.78 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.86 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.97 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.04 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.36 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.98 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.04 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.04 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.99 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.25 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.68 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.27 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.85 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.67 sec [bwa_aln_core] refine gapped alignments... 3.63 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.59 sec [bwa_aln_core] refine gapped alignments... 1.23 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.08 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.92 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.81 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.20 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.50 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.23 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.08 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.42 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.65 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.73 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.12 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.97 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.27 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.25 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.68 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.77 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.57 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.16 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.79 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.57 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.08 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.67 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.52 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.41 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.47 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.21 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.83 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.48 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.10 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.20 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.28 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.33 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.41 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.61 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.90 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.34 sec [bwa_aln_core] refine gapped alignments... 1.45 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.03 sec [bwa_aln_core] refine gapped alignments... 3.10 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.58 sec [bwa_aln_core] refine gapped alignments... 0.67 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.88 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.80 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.94 sec [bwa_aln_core] refine gapped alignments... 0.66 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.89 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.15 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.40 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 25690112 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... 0.89 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.08 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.14 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.36 sec [bwa_aln_core] refine gapped alignments... 1.30 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.30 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.02 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.41 sec [bwa_aln_core] refine gapped alignments... 1.34 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.72 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.30 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.64 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.74 sec [bwa_aln_core] refine gapped alignments... 1.40 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.74 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.91 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.43 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.73 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.64 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.32 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.08 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.17 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.60 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.89 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.27 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.82 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.04 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.63 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.04 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.98 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.21 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.80 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.95 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.52 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.46 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.50 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.76 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.72 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.09 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.43 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.53 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.78 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.56 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.56 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.75 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.03 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.07 sec [bwa_aln_core] refine gapped alignments... 2.48 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.18 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.44 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.22 sec [bwa_aln_core] refine gapped alignments... 1.43 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.18 sec [bwa_aln_core] refine gapped alignments... 1.86 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 38273024 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... 0.44 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.03 sec [bwa_aln_core] refine gapped alignments... 0.57 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.95 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.53 sec [bwa_aln_core] refine gapped alignments... 1.08 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.64 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.46 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.69 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.94 sec [bwa_aln_core] refine gapped alignments... 1.63 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.41 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.66 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.61 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.15 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.93 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.57 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.74 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.94 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.73 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.20 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.74 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.89 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.60 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.78 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.91 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.38 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 44564480 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... 0.44 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.70 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.66 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.39 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.61 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.95 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.43 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.32 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.53 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.61 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.89 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.04 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.46 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.82 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.60 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.61 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.27 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.55 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.87 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 49419522 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/SRR836496/out/align/rep1/SRR836496.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836496.fastq.gz [main] Real time: 2826.642 sec; CPU: 2713.376 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/SRR836496/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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
# SYS command. line 149
sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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-------------------- 48219 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.20 sec [bwa_aln_core] refine gapped alignments... 3.01 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.44 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.74 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.23 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.92 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.63 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.17 sec [bwa_aln_core] refine gapped alignments... 1.64 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.87 sec [bwa_aln_core] refine gapped alignments... 2.24 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.46 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.06 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.89 sec [bwa_aln_core] refine gapped alignments... 4.64 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.39 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.17 sec [bwa_aln_core] refine gapped alignments... 1.65 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.87 sec [bwa_aln_core] refine gapped alignments... 1.26 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.46 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.01 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.92 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.93 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.58 sec [bwa_aln_core] refine gapped alignments... 2.62 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.55 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.25 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.32 sec [bwa_aln_core] refine gapped alignments... 1.10 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.75 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.95 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.34 sec [bwa_aln_core] refine gapped alignments... 0.73 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.84 sec [bwa_aln_core] refine gapped alignments... 1.38 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.58 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.33 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.85 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.49 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.45 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.73 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.61 sec [bwa_aln_core] refine gapped alignments... 2.95 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.94 sec [bwa_aln_core] refine gapped alignments... 1.59 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.21 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.43 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.55 sec [bwa_aln_core] refine gapped alignments... 1.04 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.11 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.06 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.72 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.76 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.03 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.35 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.36 sec [bwa_aln_core] refine gapped alignments... 2.76 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.50 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.07 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.84 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.58 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.79 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.23 sec [bwa_aln_core] refine gapped alignments... 3.64 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.63 sec [bwa_aln_core] refine gapped alignments... 2.51 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.05 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.18 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.90 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.66 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.60 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.90 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.20 sec [bwa_aln_core] refine gapped alignments... 1.56 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.83 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.92 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.16 sec [bwa_aln_core] refine gapped alignments... 3.14 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.33 sec [bwa_aln_core] refine gapped alignments... 0.60 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.09 sec [bwa_aln_core] refine gapped alignments... 2.25 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.26 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.31 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.50 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.58 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.78 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.60 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.21 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.32 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.26 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.10 sec [bwa_aln_core] refine gapped alignments... 2.89 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.80 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.46 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.98 sec [bwa_aln_core] refine gapped alignments... 2.17 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.74 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.32 sec [bwa_aln_core] refine gapped alignments... 1.56 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.68 sec [bwa_aln_core] refine gapped alignments... 1.14 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.21 sec [bwa_aln_core] refine gapped alignments... 2.70 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.50 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.70 sec [bwa_aln_core] refine gapped alignments... 3.75 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.50 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.22 sec [bwa_aln_core] refine gapped alignments... 2.36 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.83 sec [bwa_aln_core] refine gapped alignments... 3.30 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.36 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.06 sec [bwa_aln_core] refine gapped alignments... 1.81 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.52 sec [bwa_aln_core] refine gapped alignments... 4.97 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.55 sec [bwa_aln_core] refine gapped alignments... 5.74 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.00 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.22 sec [bwa_aln_core] refine gapped alignments... 1.07 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.39 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.80 sec [bwa_aln_core] refine gapped alignments... 3.92 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.52 sec [bwa_aln_core] refine gapped alignments... 1.31 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.31 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.47 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.78 sec [bwa_aln_core] refine gapped alignments... 2.42 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.59 sec [bwa_aln_core] refine gapped alignments... 0.63 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.17 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.29 sec [bwa_aln_core] refine gapped alignments... 1.76 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.77 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.52 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.98 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.98 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.28 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.12 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.91 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.52 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.27 sec [bwa_aln_core] refine gapped alignments... 1.53 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.78 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.23 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.94 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.67 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.67 sec [bwa_aln_core] refine gapped alignments... 2.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.56 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.43 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.49 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.62 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.90 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.93 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.50 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.07 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/SRR836496/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: 2336.515 sec; CPU: 2252.800 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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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-------------------- 5738 (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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 1148 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Nov 02 06:11:25 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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 06:11:25 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 06:11:25 MarkDuplicates Start of doWork freeMemory: 254881984; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-11-02 06:11:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-02 06:11:25 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. INFO 2016-11-02 06:11:31 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 06:11:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 5s. Last read position: chr2:120,600,340 INFO 2016-11-02 06:11:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:42 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 5s. Last read position: chr3:96,659,413 INFO 2016-11-02 06:11:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:47 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 5s. Last read position: chr4:108,195,091 INFO 2016-11-02 06:11:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 5s. Last read position: chr5:103,594,339 INFO 2016-11-02 06:11:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:11:58 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 5s. Last read position: chr6:98,592,333 INFO 2016-11-02 06:11:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:04 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 5s. Last read position: chr7:114,109,505 INFO 2016-11-02 06:12:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:12 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 7s. Last read position: chr8:121,515,352 INFO 2016-11-02 06:12:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:19 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 6s. Last read position: chr10:14,536,964 INFO 2016-11-02 06:12:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:24 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 5s. Last read position: chr11:32,924,585 INFO 2016-11-02 06:12:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:29 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 5s. Last read position: chr12:41,050,039 INFO 2016-11-02 06:12:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:34 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 4s. Last read position: chr13:80,878,598 INFO 2016-11-02 06:12:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:39 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 5s. Last read position: chr15:12,027,335 INFO 2016-11-02 06:12:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:12:47 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 8s. Last read position: chr16:56,024,589 INFO 2016-11-02 06:12:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:13:06 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 18s. Last read position: chr18:10,030,498 INFO 2016-11-02 06:13:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:13:11 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 4s. Last read position: chrX:36,565,109 INFO 2016-11-02 06:13:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 06:13:13 MarkDuplicates Read 16572675 records. 0 pairs never matched. INFO 2016-11-02 06:13:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 1985858600; totalMemory: 2059403264; maxMemory: 3817865216 INFO 2016-11-02 06:13:15 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk. INFO 2016-11-02 06:13:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-02 06:13:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-02 06:13:23 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-02 06:13:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 1390380368; totalMemory: 2359820288; maxMemory: 3817865216 INFO 2016-11-02 06:13:24 MarkDuplicates Marking 13188493 records as duplicates. INFO 2016-11-02 06:13:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-02 06:15:34 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:10s. Time for last 10,000,000: 130s. Last read position: chr11:32,924,585 INFO 2016-11-02 06:16:58 MarkDuplicates Before output close freeMemory: 2095855576; totalMemory: 2113404928; maxMemory: 3817865216 INFO 2016-11-02 06:16:59 MarkDuplicates After output close freeMemory: 2072261560; totalMemory: 2089811968; maxMemory: 3817865216 [Wed Nov 02 06:16:59 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 5.56 minutes. Runtime.totalMemory()=2089811968 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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/SRR836496/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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/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/SRR836496/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/SRR836496/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-------------------- 25855 (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/SRR836496/out/align/rep1/SRR836496.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.bam | \
sambamba sort -t 3 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21917 (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/SRR836496/out/align/rep1/SRR836496.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.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-------------------- 31029 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Nov 02 07:18:54 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.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 07:18:54 PDT 2016] Executing as imk1@surya on Linux 4.4.0-31-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-02 07:18:54 MarkDuplicates Start of doWork freeMemory: 254882272; totalMemory: 257425408; maxMemory: 3817865216 INFO 2016-11-02 07:18:54 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-02 07:18:54 MarkDuplicates Will retain up to 14684096 data points before spilling to disk. WARNING 2016-11-02 07:18:54 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836496.44626759'. 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 07:18:58 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:81,497,891 INFO 2016-11-02 07:18:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:01 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:156,373,759 INFO 2016-11-02 07:19:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:04 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr2:29,327,811 INFO 2016-11-02 07:19:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:08 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr2:98,662,618 INFO 2016-11-02 07:19:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:11 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr2:164,403,141 INFO 2016-11-02 07:19:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:14 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr3:64,804,771 INFO 2016-11-02 07:19:14 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:17 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr3:135,741,224 INFO 2016-11-02 07:19:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr4:57,297,839 INFO 2016-11-02 07:19:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:25 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr4:132,535,691 INFO 2016-11-02 07:19:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:29 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 4s. Last read position: chr5:44,247,081 INFO 2016-11-02 07:19:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:32 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr5:119,992,830 INFO 2016-11-02 07:19:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:35 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr6:36,935,243 INFO 2016-11-02 07:19:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:39 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 4s. Last read position: chr6:110,890,757 INFO 2016-11-02 07:19:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:41 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr7:43,405,185 INFO 2016-11-02 07:19:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 13s. Last read position: chr7:114,737,911 INFO 2016-11-02 07:19:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:19:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr8:41,336,619 INFO 2016-11-02 07:19:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:00 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr8:114,499,212 INFO 2016-11-02 07:20:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:03 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr9:55,429,420 INFO 2016-11-02 07:20:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:06 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr9:119,003,229 INFO 2016-11-02 07:20:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr10:68,673,661 INFO 2016-11-02 07:20:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:12 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr11:6,629,952 INFO 2016-11-02 07:20:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:17 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 4s. Last read position: chr11:73,067,677 INFO 2016-11-02 07:20:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:19 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr12:4,769,319 INFO 2016-11-02 07:20:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:22 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr12:84,653,563 INFO 2016-11-02 07:20:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:25 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr13:40,298,538 INFO 2016-11-02 07:20:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:27 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr13:112,509,711 INFO 2016-11-02 07:20:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:30 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr14:73,345,848 INFO 2016-11-02 07:20:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:32 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr15:33,624,844 INFO 2016-11-02 07:20:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:34 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr15:99,225,442 INFO 2016-11-02 07:20:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:40 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 6s. Last read position: chr16:65,636,532 INFO 2016-11-02 07:20:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:43 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr17:39,843,917 INFO 2016-11-02 07:20:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:46 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr18:20,690,709 INFO 2016-11-02 07:20:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:48 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr19:3,851,781 INFO 2016-11-02 07:20:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:51 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chrX:20,796,431 INFO 2016-11-02 07:20:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-02 07:20:54 MarkDuplicates Read 34842548 records. 0 pairs never matched. INFO 2016-11-02 07:20:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 1340536880; totalMemory: 1412431872; maxMemory: 3817865216 INFO 2016-11-02 07:20:55 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk. INFO 2016-11-02 07:20:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-02 07:20:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-02 07:21:04 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-02 07:21:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 1793412552; totalMemory: 2761424896; maxMemory: 3817865216 INFO 2016-11-02 07:21:04 MarkDuplicates Marking 8239587 records as duplicates. INFO 2016-11-02 07:21:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-02 07:22:17 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:13s. Time for last 10,000,000: 73s. Last read position: chr5:44,247,081 INFO 2016-11-02 07:23:31 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 74s. Last read position: chr10:68,673,661 INFO 2016-11-02 07:24:49 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:03:44s. Time for last 10,000,000: 77s. Last read position: chr16:65,636,532 INFO 2016-11-02 07:25:26 MarkDuplicates Before output close freeMemory: 2583704152; totalMemory: 2601517056; maxMemory: 3817865216 INFO 2016-11-02 07:25:26 MarkDuplicates After output close freeMemory: 2583703096; totalMemory: 2601517056; maxMemory: 3817865216 [Wed Nov 02 07:25:26 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.54 minutes. Runtime.totalMemory()=2601517056 | ||||||||||||||||||||||||||||||||||||||||
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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/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 7313 (process ID) old priority 0, new priority 10 Waiting for 40 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/SRR836496/out/align/rep1/SRR836496.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.bam
# SYS command. line 153
sambamba index -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.bam
# SYS command. line 155
sambamba flagstat -t 3 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.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/SRR836496/out/qc/rep1/SRR836496.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-------------------- 8584 (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/SRR836496/out/align/rep1/SRR836496.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 13081 (process ID) old priority 0, new priority 10 Waiting for 3 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 $$
# SYS command. line 46
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.15M.tagAlign.gz
# SYS command. line 49
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 13247 (process ID) old priority 0, new priority 10 Waiting for 32 seconds. | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 249
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 252
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz | wc -l )
# SYS command. line 253
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 257
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.
# SYS command. line 260
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.pr1.tagAlign.gz
# SYS command. line 261
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.00
# SYS command. line 262
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr2/SRR836496.nodup.pr2.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/pseudo_reps/rep1/pr1/SRR836496.nodup.01
# SYS command. line 265
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 13252 (process ID) old priority 0, new priority 10 Waiting for 3 seconds. | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# 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 ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/align/rep1/SRR836496.nodup.15M.tagAlign.gz -p=3 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out/qc/rep1/SRR836496.nodup.15M.cc.qc
# SYS command. line 222
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
41784 (process ID) old priority 0, new priority 10
--------------------Post mortem info--------------------
==============================================================
job_number: 3297
submission_time: Wed Nov 2 07:37:41 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/SRR836496
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/chipseq.bds.20161101_222026_772_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/SRR836496/chipseq.bds.20161101_222026_772_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=37634.SRR836496.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/SRR836496,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, SRR836496, -nth, 5, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/SRR836496/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/SRR836496.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/SRR836496 |
| 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/SRR836496 |
| 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 | 37634.SRR836496.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 |