| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161110_171041_880 |
| Start time | 2016-11-10 17:10:41 |
| Run time | 04:33:45.432 |
| Tasks executed | 4 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 bwa_sam rep1 |
| Arguments* | [-title, SRR1370904_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370904_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_41 | thread_Root | chipseq.bds.20161110_171041_880_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161110_171041_880_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 |
| thread_42 | thread_Root | chipseq.bds.20161110_171041_880_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161110_171041_880_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
|
|
# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${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/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370904_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/rep1/SRR1370904_1.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-------------------- 12951 (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] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.87 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.04 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.87 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.52 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.89 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.90 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.20 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.48 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.16 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.57 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.30 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.88 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.32 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.25 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.64 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.38 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.81 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.17 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.71 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 182.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 147.48 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.08 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.67 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.93 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.23 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.29 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.28 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.49 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.23 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.34 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.45 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.45 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 106.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.72 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.14 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.75 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 99.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.17 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.28 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.95 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.21 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.74 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.53 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.93 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.36 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.92 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.81 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.10 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.24 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.40 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.88 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 112.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.15 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 100.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.11 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.30 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.75 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.27 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.32 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.33 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.96 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.67 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.05 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.87 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.06 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 31445752 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/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370904_1.fastq.gz [main] Real time: 10455.699 sec; CPU: 10166.780 sec | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 6823 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
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 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
19203 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Thu Nov 10 19:57:27 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/qc/ctl1/ss_50M_2000_GRCh38.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
[Thu Nov 10 19:57:27 PST 2016] Executing as imk1@wotan on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-10 19:57:31 MarkDuplicates Start of doWork freeMemory: 254877736; totalMemory: 257425408; maxMemory: 11453595648
INFO 2016-11-10 19:57:31 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-10 19:57:31 MarkDuplicates Will retain up to 44052290 data points before spilling to disk.
INFO 2016-11-10 19:57:52 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:22,298,551
INFO 2016-11-10 19:57:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 19:58:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 16s. Last read position: chr1:41,895,424
INFO 2016-11-10 19:58:08 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 19:58:22 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 13s. Last read position: chr1:63,396,527
INFO 2016-11-10 19:58:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 19:58:41 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 19s. Last read position: chr1:89,147,707
INFO 2016-11-10 19:58:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 19:58:55 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 13s. Last read position: chr1:115,615,553
INFO 2016-11-10 19:58:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 19:59:06 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 10s. Last read position: chr1:164,468,682
INFO 2016-11-10 19:59:06 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 19:59:22 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 16s. Last read position: chr1:189,102,252
INFO 2016-11-10 19:59:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 19:59:34 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 12s. Last read position: chr1:213,979,760
INFO 2016-11-10 19:59:34 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 19:59:46 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 12s. Last read position: chr1:231,814,268
INFO 2016-11-10 19:59:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 19:59:57 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 11s. Last read position: chr2:3,652,468
INFO 2016-11-10 19:59:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:00:13 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 15s. Last read position: chr2:39,505,122
INFO 2016-11-10 20:00:13 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:00:24 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 11s. Last read position: chr2:73,561,393
INFO 2016-11-10 20:00:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:00:37 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 12s. Last read position: chr2:120,526,571
INFO 2016-11-10 20:00:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:00:46 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 9s. Last read position: chr2:160,316,783
INFO 2016-11-10 20:00:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:01:11 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 24s. Last read position: chr2:195,549,735
INFO 2016-11-10 20:01:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:01:23 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 12s. Last read position: chr2:230,358,034
INFO 2016-11-10 20:01:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:01:46 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 22s. Last read position: chr3:16,305,780
INFO 2016-11-10 20:01:46 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:02:15 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 29s. Last read position: chr3:49,251,279
INFO 2016-11-10 20:02:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:02:42 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 27s. Last read position: chr3:84,621,225
INFO 2016-11-10 20:02:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:03:16 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 34s. Last read position: chr3:128,121,129
INFO 2016-11-10 20:03:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:03:46 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 29s. Last read position: chr3:165,373,238
INFO 2016-11-10 20:03:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:04:17 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 31s. Last read position: chr3:195,333,247
INFO 2016-11-10 20:04:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:04:52 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 34s. Last read position: chr4:37,752,582
INFO 2016-11-10 20:04:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:05:56 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 64s. Last read position: chr4:81,286,306
INFO 2016-11-10 20:05:56 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:06:50 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 53s. Last read position: chr4:119,339,736
INFO 2016-11-10 20:06:50 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:07:32 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 42s. Last read position: chr4:158,818,783
INFO 2016-11-10 20:07:32 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:08:21 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 48s. Last read position: chr5:6,447,551
INFO 2016-11-10 20:08:21 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-10 20:09:17 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 55s. Last read position: chr5:33,219,021
INFO 2016-11-10 20:09:17 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:10:12 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 54s. Last read position: chr5:60,694,078
INFO 2016-11-10 20:10:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:10:56 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 44s. Last read position: chr5:86,336,676
INFO 2016-11-10 20:10:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:11:37 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 41s. Last read position: chr5:112,930,184
INFO 2016-11-10 20:11:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:12:17 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 40s. Last read position: chr5:136,852,889
INFO 2016-11-10 20:12:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:13:43 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 86s. Last read position: chr5:160,271,193
INFO 2016-11-10 20:13:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:14:24 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 40s. Last read position: chr6:4,126,386
INFO 2016-11-10 20:14:24 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:14:59 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:17:26s. Time for last 1,000,000: 35s. Last read position: chr6:28,666,579
INFO 2016-11-10 20:14:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:15:43 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 43s. Last read position: chr6:49,527,281
INFO 2016-11-10 20:15:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:16:12 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 29s. Last read position: chr6:81,728,195
INFO 2016-11-10 20:16:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:16:46 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 33s. Last read position: chr6:107,535,760
INFO 2016-11-10 20:16:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:17:23 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:19:49s. Time for last 1,000,000: 37s. Last read position: chr6:132,364,408
INFO 2016-11-10 20:17:23 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:18:01 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:20:27s. Time for last 1,000,000: 37s. Last read position: chr6:156,918,595
INFO 2016-11-10 20:18:01 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:18:41 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:21:07s. Time for last 1,000,000: 40s. Last read position: chr7:18,636,743
INFO 2016-11-10 20:18:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:19:12 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:21:38s. Time for last 1,000,000: 30s. Last read position: chr7:53,850,313
INFO 2016-11-10 20:19:12 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:23:01 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:25:27s. Time for last 1,000,000: 229s. Last read position: chr7:96,503,433
INFO 2016-11-10 20:23:01 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:25:16 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:27:42s. Time for last 1,000,000: 135s. Last read position: chr7:120,651,846
INFO 2016-11-10 20:25:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:27:28 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:29:54s. Time for last 1,000,000: 132s. Last read position: chr7:146,401,497
INFO 2016-11-10 20:27:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:28:51 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:31:17s. Time for last 1,000,000: 82s. Last read position: chr8:17,030,519
INFO 2016-11-10 20:28:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:31:34 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:34:01s. Time for last 1,000,000: 163s. Last read position: chr8:42,750,671
INFO 2016-11-10 20:31:34 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:32:55 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:35:21s. Time for last 1,000,000: 80s. Last read position: chr8:85,385,487
INFO 2016-11-10 20:32:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:36:42 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:39:09s. Time for last 1,000,000: 227s. Last read position: chr8:124,358,985
INFO 2016-11-10 20:36:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:37:42 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:40:08s. Time for last 1,000,000: 59s. Last read position: chr9:18,183,883
INFO 2016-11-10 20:37:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:39:33 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:41:59s. Time for last 1,000,000: 111s. Last read position: chr9:84,163,983
INFO 2016-11-10 20:39:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:41:06 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:43:32s. Time for last 1,000,000: 92s. Last read position: chr9:119,875,535
INFO 2016-11-10 20:41:06 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:42:01 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:44:27s. Time for last 1,000,000: 55s. Last read position: chr10:5,661,683
INFO 2016-11-10 20:42:01 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 20:44:32 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:46:58s. Time for last 1,000,000: 150s. Last read position: chr10:29,748,948
INFO 2016-11-10 20:44:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:45:26 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:47:52s. Time for last 1,000,000: 54s. Last read position: chr10:61,280,221
INFO 2016-11-10 20:45:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:46:49 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:49:16s. Time for last 1,000,000: 83s. Last read position: chr10:85,305,552
INFO 2016-11-10 20:46:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 20:48:46 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:51:12s. Time for last 1,000,000: 116s. Last read position: chr10:108,129,202
INFO 2016-11-10 20:48:46 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:51:14 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:53:40s. Time for last 1,000,000: 148s. Last read position: chr10:132,730,123
INFO 2016-11-10 20:51:14 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:53:42 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:56:08s. Time for last 1,000,000: 147s. Last read position: chr11:35,359,267
INFO 2016-11-10 20:53:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 20:56:03 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:58:29s. Time for last 1,000,000: 141s. Last read position: chr11:75,696,431
INFO 2016-11-10 20:56:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 20:58:01 MarkDuplicates Read 61,000,000 records. Elapsed time: 01:00:27s. Time for last 1,000,000: 117s. Last read position: chr11:114,414,621
INFO 2016-11-10 20:58:01 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 20:58:58 MarkDuplicates Read 62,000,000 records. Elapsed time: 01:01:24s. Time for last 1,000,000: 56s. Last read position: chr12:8,900,276
INFO 2016-11-10 20:58:58 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 21:01:50 MarkDuplicates Read 63,000,000 records. Elapsed time: 01:04:16s. Time for last 1,000,000: 172s. Last read position: chr12:38,863,889
INFO 2016-11-10 21:01:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:07:27 MarkDuplicates Read 64,000,000 records. Elapsed time: 01:09:54s. Time for last 1,000,000: 337s. Last read position: chr12:60,598,824
INFO 2016-11-10 21:07:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 21:08:27 MarkDuplicates Read 65,000,000 records. Elapsed time: 01:10:53s. Time for last 1,000,000: 59s. Last read position: chr12:88,520,538
INFO 2016-11-10 21:08:27 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 21:10:46 MarkDuplicates Read 66,000,000 records. Elapsed time: 01:13:13s. Time for last 1,000,000: 139s. Last read position: chr12:112,268,437
INFO 2016-11-10 21:10:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 21:11:46 MarkDuplicates Read 67,000,000 records. Elapsed time: 01:14:12s. Time for last 1,000,000: 59s. Last read position: chr13:23,999,632
INFO 2016-11-10 21:11:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 21:15:29 MarkDuplicates Read 68,000,000 records. Elapsed time: 01:17:55s. Time for last 1,000,000: 222s. Last read position: chr13:51,165,870
INFO 2016-11-10 21:15:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 21:17:31 MarkDuplicates Read 69,000,000 records. Elapsed time: 01:19:57s. Time for last 1,000,000: 122s. Last read position: chr13:88,986,369
INFO 2016-11-10 21:17:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:24:21 MarkDuplicates Read 70,000,000 records. Elapsed time: 01:26:47s. Time for last 1,000,000: 409s. Last read position: chr14:23,149,367
INFO 2016-11-10 21:24:21 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 21:27:51 MarkDuplicates Read 71,000,000 records. Elapsed time: 01:30:17s. Time for last 1,000,000: 210s. Last read position: chr14:58,140,905
INFO 2016-11-10 21:27:51 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:28:54 MarkDuplicates Read 72,000,000 records. Elapsed time: 01:31:20s. Time for last 1,000,000: 63s. Last read position: chr14:91,912,553
INFO 2016-11-10 21:28:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 21:31:29 MarkDuplicates Read 73,000,000 records. Elapsed time: 01:33:56s. Time for last 1,000,000: 155s. Last read position: chr15:38,895,095
INFO 2016-11-10 21:31:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 21:36:39 MarkDuplicates Read 74,000,000 records. Elapsed time: 01:39:06s. Time for last 1,000,000: 310s. Last read position: chr15:68,188,367
INFO 2016-11-10 21:36:39 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 21:38:04 MarkDuplicates Read 75,000,000 records. Elapsed time: 01:40:31s. Time for last 1,000,000: 84s. Last read position: chr15:87,921,272
INFO 2016-11-10 21:38:04 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
--------------------Post mortem info--------------------
==============================================================
job_number: 7164
exec_file: job_scripts/7164
submission_time: Thu Nov 10 17:47:40 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /software/ascp/:/software/sratoolkit/2.5.2/bin/:/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/chipseq.bds.20161110_171041_880_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/chipseq.bds.20161110_171041_880_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_12.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,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=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=32454.SRR1370904_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,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,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 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,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
parallel environment: shm range: 1
usage 1: cpu=00:19:09, mem=3906.62294 GBs, io=8.20246, vmem=3.514G, maxvmem=3.514G
scheduling info: queue instance "amd.q@wotan" dropped because it is full
queue instance "q@kadru" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@surya" dropped because it is full
| ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/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/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/rep1/SRR1370904_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370904_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/rep1/SRR1370904_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/align/rep1/SRR1370904_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out/qc/rep1/SRR1370904_1.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-------------------- 35836 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.01 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences. 0.57 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.89 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.17 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.87 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.51 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.54 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.61 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.77 sec [bwa_aln_core] refine gapped alignments... 0.96 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.63 sec [bwa_aln_core] refine gapped alignments... 1.36 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.03 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.51 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.79 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.96 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.62 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.84 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.46 sec [bwa_aln_core] refine gapped alignments... 1.07 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.45 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.44 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.22 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.55 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.05 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.57 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.82 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.07 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.72 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.66 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.92 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.55 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.76 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.29 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.10 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.24 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.88 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.55 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.68 sec [bwa_aln_core] refine gapped alignments... 0.73 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.34 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.13 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| string | _LMFILES_ | /software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6 |
| bool | allowEmpty | false |
| string[] | args | [-title, SRR1370904_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370904_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $] |
| string | ASCPKEY | /software/ascp/etc/asperaweb_id_dsa.openssh |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DERBY_HOME | /usr/lib/jvm/java-8-oracle/db |
| string | DISPLAY | localhost:12.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| string | J2REDIR | /usr/lib/jvm/java-8-oracle/jre |
| string | J2SDKDIR | /usr/lib/jvm/java-8-oracle |
| string | JAVA_HOME | /usr/lib/jvm/java-8-oracle |
| int | K | 1024 |
| string | KERAS_DIR | /users/imk1/.local/lib/python2.7/site-packages/keras/ |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_N5SeQf |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6 |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESAPPSDIR | /software |
| 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 | /software/ascp/:/software/sratoolkit/2.5.2/bin/:/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/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/HughesZnfData/SRR1370904_1 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370904_1 |
| 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 55144 22 |
| string | SSH_CONNECTION | 171.65.77.8 55144 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/4 |
| string | STY | 32454.SRR1370904_1.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 | 20 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |