| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20160929_154136_675 |
| Start time | 2016-09-29 15:41:36 |
| Run time | 18:24:09.768 |
| Tasks executed | 10 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-title, ZF8, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF8_allReps.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 | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20160929_154136_675/task.callpeak_spp.spp_rep1.line_54.id_16 chipseq.bds.20160929_154136_675/task.callpeak_idr.idr_final_qc.line_205.id_17 chipseq.bds.20160929_154136_675/task.graphviz.report.line_97.id_18 chipseq.bds.20160929_154136_675/task.report.pdf2png.line_324.id_23 |
| thread_41 | thread_Root | |
| thread_42 | thread_Root | chipseq.bds.20160929_154136_675_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10 chipseq.bds.20160929_154136_675_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_11 chipseq.bds.20160929_154136_675_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_12 chipseq.bds.20160929_154136_675_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_13 chipseq.bds.20160929_154136_675_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_14 chipseq.bds.20160929_154136_675_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_15 |
| 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 1 /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/ZF8/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-------------------- 39780 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.04 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.98 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.77 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.03 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.65 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.27 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.56 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.93 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.47 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.81 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.93 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.69 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.96 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.01 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.68 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.10 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... 71.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.99 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.89 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.79 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.99 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.33 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... 49.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 8.20 sec [bwa_aln_core] write to the disk... 0.00 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 1 /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: 6704.369 sec; CPU: 6707.724 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/ZF8/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 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/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-------------------- 32881 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.57 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.04 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.97 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.05 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.05 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.98 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.69 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.35 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.18 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.14 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.66 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.68 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.80 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.58 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.35 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.15 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.32 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.62 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.36 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.29 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.15 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.16 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.21 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.30 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.54 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.18 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.69 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.33 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.47 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.48 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.01 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.53 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.15 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.35 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.42 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.25 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.15 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.22 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.00 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.05 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.49 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.04 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.19 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.24 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.10 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.30 sec [bwa_aln_core] print alignments... 0.09 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/ZF8/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: 755.402 sec; CPU: 581.892 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/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 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/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/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/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-------------------- 51033 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 2846 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Thu Sep 29 18:05:09 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Sep 29 18:05:09 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory) INFO 2016-09-29 18:05:09 MarkDuplicates Start of doWork freeMemory: 255389880; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-29 18:05:09 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-29 18:05:09 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. INFO 2016-09-29 18:05:13 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:169,651,309 INFO 2016-09-29 18:05:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:16 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr2:120,600,340 INFO 2016-09-29 18:05:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:19 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr3:96,659,413 INFO 2016-09-29 18:05:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:22 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr4:108,195,091 INFO 2016-09-29 18:05:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:26 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr5:103,594,339 INFO 2016-09-29 18:05:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:29 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr6:98,592,333 INFO 2016-09-29 18:05:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:32 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr7:114,109,505 INFO 2016-09-29 18:05:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:37 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr8:121,515,352 INFO 2016-09-29 18:05:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:41 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 4s. Last read position: chr10:14,536,964 INFO 2016-09-29 18:05:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr11:32,924,585 INFO 2016-09-29 18:05:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:47 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr12:41,050,039 INFO 2016-09-29 18:05:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:50 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr13:80,878,598 INFO 2016-09-29 18:05:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:53 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr15:12,027,335 INFO 2016-09-29 18:05:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:05:56 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: chr16:56,024,589 INFO 2016-09-29 18:05:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:06:02 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 5s. Last read position: chr18:10,030,498 INFO 2016-09-29 18:06:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:06:11 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 9s. Last read position: chrX:36,565,109 INFO 2016-09-29 18:06:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 18:06:13 MarkDuplicates Read 16572675 records. 0 pairs never matched. INFO 2016-09-29 18:06:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 1966737896; totalMemory: 2039480320; maxMemory: 3817799680 INFO 2016-09-29 18:06:14 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-29 18:06:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-29 18:06:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-29 18:06:18 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-29 18:06:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 918385544; totalMemory: 1885339648; maxMemory: 3817799680 INFO 2016-09-29 18:06:19 MarkDuplicates Marking 13188493 records as duplicates. INFO 2016-09-29 18:06:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-29 18:08:15 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:56s. Time for last 10,000,000: 116s. Last read position: chr11:32,924,585 INFO 2016-09-29 18:09:31 MarkDuplicates Before output close freeMemory: 1961833984; totalMemory: 1976434688; maxMemory: 3817799680 INFO 2016-09-29 18:09:32 MarkDuplicates After output close freeMemory: 1976185528; totalMemory: 1990787072; maxMemory: 3817799680 [Thu Sep 29 18:09:32 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 4.38 minutes. Runtime.totalMemory()=1990787072 | ||||||||||||||||||||||||||||||||||||||||
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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/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/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/ZF8/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/ZF8/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-------------------- 52038 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 506
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 509
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 52421 (process ID) old priority 0, new priority 10 Waiting for 52 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 59
if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 63
Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/rep1/ZF8_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1 -speak=130 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
26179 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/rep1/ZF8_allReps.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 130
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_VS_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/peak/spp/rep1/ZF8_allReps.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/rep1/ZF8_allReps.nodup.tagAlign.gz
opened /tmp/9887.1.q/RtmpLHG0ap/ZF8_allReps.nodup.tagAlign6685e5de9e6
done. read 36695744 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
opened /tmp/9887.1.q/RtmpLHG0ap/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign668543b754a0
done. read 3384182 fragments
Control data read length 50
Calculating peak characteristics
Minimum cross-correlation value 0.3483066
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.465110251923974
Top 3 estimates for fragment length 130
Window half size 440
Phantom peak location 55
Phantom peak Correlation 0.4440836
Normalized Strand cross-correlation coefficient (NSC) 1.335347
Relative Strand Cross correlation Coefficient (RSC) 1.219537
Phantom Peak Quality Tag 1
null device
1
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.1113835 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 8.97799 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000202
Detected 1874112 peaks
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 36 warnings (use warnings() to see them)
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# SYS command. line 207
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 209
echo -e "Nt\t""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/ZF8_IDR_final.qc
# SYS command. line 210
echo -e "0\t""0\tN/A\tN/A\tNaN\tNaN\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/ZF8_IDR_final.qc
# SYS command. line 212
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 29484 (process ID) old priority 0, new priority 10 Waiting for 60 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 98
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/report/ZF8_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/report/ZF8_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/report/ZF8_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 54497 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 325
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 326
gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/rep1/ZF8_allReps.nodup.15M.cc.plot.png \
-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out/qc/rep1/ZF8_allReps.nodup.15M.cc.plot.pdf
--------------------Stdout-------------------- 54538 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, ZF8, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF8/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF8_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DISPLAY | localhost:19.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/keras |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_eHVWt0 |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5 |
| string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF8 |
| 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/ZF8 |
| string | PYTHONPATH | /software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SGE_CELL | default |
| string | SGE_ROOT | /var/lib/gridengine |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 58475 22 |
| string | SSH_CONNECTION | 171.65.77.8 58475 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/38 |
| string | STY | 39652.ZF8.BDS |
| string | system | sge |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
| int | timeout | -1 |
| string | USER | imk1 |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1048 |
| string | XDG_SESSION_ID | 418 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |