| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161109_175122_896 |
| Start time | 2016-11-09 17:51:22 |
| Run time | 18:57:45.326 |
| Tasks executed | 3 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 bwa_aln rep1 |
| Arguments* | [-title, SRR1370894_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370894_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_42 | thread_Root | chipseq.bds.20161109_175122_896_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161109_175122_896_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12 |
| thread_41 | thread_Root | chipseq.bds.20161109_175122_896_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 |
| 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/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370894_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/rep1/SRR1370894_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-------------------- 5184 (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] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.58 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.54 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.90 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.41 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.48 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.36 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.79 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.65 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.49 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.53 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.89 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.62 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.50 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.18 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.64 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.03 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.56 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.26 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.13 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 0.4% 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] 25952256 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 0.3% 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] 26738688 sequences have been processed. [bwa_read_seq] 0.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.70 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 0.7% 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] 27525120 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 5.37 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 27549070 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/SRR1370894_1.fastq.gz [main] Real time: 4992.748 sec; CPU: 4990.228 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 52183 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stderr--------------------
INFO 2016-11-09 21:21:17 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr1:22,298,551
|
| 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, SRR1370894_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370894_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370894_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/SRR1370894_1 |
| 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/HughesZnfData/SRR1370894_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 | 14206.SRR1370894_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 |